Antarctica - ASV analysis

Get the Antarctica ASVs

set id description
16 Antar_2015_18S_V4
17 Antar_2015_16S_plastid
18 Antar_2015_18S_V4_sorted
  • Only use asv for which supergroup_boot >= 90
  • Only keep photosynthetic groups abd exclude dinoflagellates
Phyloseq - 18S filter
phyloseq-class experiment-level object
otu_table()   OTU Table:         [ 707 taxa and 123 samples ]
sample_data() Sample Data:       [ 123 samples by 61 sample variables ]
tax_table()   Taxonomy Table:    [ 707 taxa by 8 taxonomic ranks ]
============================
Phyloseq - 16S plastid
phyloseq-class experiment-level object
otu_table()   OTU Table:         [ 419 taxa and 103 samples ]
sample_data() Sample Data:       [ 103 samples by 61 sample variables ]
tax_table()   Taxonomy Table:    [ 419 taxa by 8 taxonomic ranks ]
============================
Phyloseq - 18S sort
phyloseq-class experiment-level object
otu_table()   OTU Table:         [ 264 taxa and 60 samples ]
sample_data() Sample Data:       [ 60 samples by 61 sample variables ]
tax_table()   Taxonomy Table:    [ 264 taxa by 8 taxonomic ranks ]
============================
 [1] "sample_id"                      "file_name"                     
 [3] "sample_name"                    "sample_code"                   
 [5] "metadata_code"                  "replicate"                     
 [7] "DNA_RNA"                        "fraction_name"                 
 [9] "fraction_min"                   "fraction_max"                  
[11] "sample_concentration"           "sample_sorted"                 
[13] "reads_total"                    "sample_remark"                 
[15] "metadata_id"                    "metadata_code_original"        
[17] "project"                        "cruise"                        
[19] "station_id"                     "station_id_num"                
[21] "year"                           "date"                          
[23] "time"                           "season"                        
[25] "depth_level"                    "depth"                         
[27] "substrate"                      "substrate_description"         
[29] "substrate_description_detailed" "experiment_name"               
[31] "experiment_time"                "experiment_time_unit"          
[33] "experiment_bottle"              "experiment_condition"          
[35] "latitude"                       "longitude"                     
[37] "site_name"                      "country"                       
[39] "oceanic_region"                 "bottom_depth"                  
[41] "temperature"                    "salinity"                      
[43] "pH"                             "O2"                            
[45] "fluorescence"                   "ice_coverage"                  
[47] "Chla"                           "NO2"                           
[49] "NO3"                            "PO4"                           
[51] "Si"                             "Chla_0.2_3 um"                 
[53] "bact_ml"                        "syn_ml"                        
[55] "peuk_ml"                        "neuk_ml"                       
[57] "crypto_ml"                      "virus_small_ml"                
[59] "virus_large_ml"                 "metadata_remark"               
[61] "sample_label"                  

Get the different fraction separately

Phyloseq - 18S filter 0.2 um
phyloseq-class experiment-level object
otu_table()   OTU Table:         [ 331 taxa and 43 samples ]
sample_data() Sample Data:       [ 43 samples by 61 sample variables ]
tax_table()   Taxonomy Table:    [ 331 taxa by 8 taxonomic ranks ]
============================
Phyloseq - 18S filter 3 um
phyloseq-class experiment-level object
otu_table()   OTU Table:         [ 377 taxa and 44 samples ]
sample_data() Sample Data:       [ 44 samples by 61 sample variables ]
tax_table()   Taxonomy Table:    [ 377 taxa by 8 taxonomic ranks ]
============================
Phyloseq - 18S filter 20 um
phyloseq-class experiment-level object
otu_table()   OTU Table:         [ 310 taxa and 36 samples ]
sample_data() Sample Data:       [ 36 samples by 61 sample variables ]
tax_table()   Taxonomy Table:    [ 310 taxa by 8 taxonomic ranks ]
============================
Phyloseq - 16S plastid 0.2 um
phyloseq-class experiment-level object
otu_table()   OTU Table:         [ 183 taxa and 29 samples ]
sample_data() Sample Data:       [ 29 samples by 61 sample variables ]
tax_table()   Taxonomy Table:    [ 183 taxa by 8 taxonomic ranks ]
============================
Phyloseq - 16S plastid 3 um
phyloseq-class experiment-level object
otu_table()   OTU Table:         [ 219 taxa and 42 samples ]
sample_data() Sample Data:       [ 42 samples by 61 sample variables ]
tax_table()   Taxonomy Table:    [ 219 taxa by 8 taxonomic ranks ]
============================
Phyloseq - 16S plastid 20 um
phyloseq-class experiment-level object
otu_table()   OTU Table:         [ 212 taxa and 32 samples ]
sample_data() Sample Data:       [ 32 samples by 61 sample variables ]
tax_table()   Taxonomy Table:    [ 212 taxa by 8 taxonomic ranks ]
============================
Phyloseq - 18S sort pico
phyloseq-class experiment-level object
otu_table()   OTU Table:         [ 185 taxa and 30 samples ]
sample_data() Sample Data:       [ 30 samples by 61 sample variables ]
tax_table()   Taxonomy Table:    [ 185 taxa by 8 taxonomic ranks ]
============================
Phyloseq - 18S sort nano
phyloseq-class experiment-level object
otu_table()   OTU Table:         [ 132 taxa and 30 samples ]
sample_data() Sample Data:       [ 30 samples by 61 sample variables ]
tax_table()   Taxonomy Table:    [ 132 taxa by 8 taxonomic ranks ]
============================

Surface samples

  • Only use Station 6 (not 14)
  • Only surface considered (5 m)
  • Do not consider TFF samples
  • Very important, must remove taxa that are not present in the filtered samples
Phyloseq - 18S filter surface
phyloseq-class experiment-level object
otu_table()   OTU Table:         [ 394 taxa and 50 samples ]
sample_data() Sample Data:       [ 50 samples by 61 sample variables ]
tax_table()   Taxonomy Table:    [ 394 taxa by 8 taxonomic ranks ]
============================
Phyloseq - 16S plastid surface
phyloseq-class experiment-level object
otu_table()   OTU Table:         [ 236 taxa and 40 samples ]
sample_data() Sample Data:       [ 40 samples by 61 sample variables ]
tax_table()   Taxonomy Table:    [ 236 taxa by 8 taxonomic ranks ]
============================
Phyloseq - 18S sort surface
phyloseq-class experiment-level object
otu_table()   OTU Table:         [ 114 taxa and 16 samples ]
sample_data() Sample Data:       [ 16 samples by 61 sample variables ]
tax_table()   Taxonomy Table:    [ 114 taxa by 8 taxonomic ranks ]
============================
Phyloseq - 18S filter 0.2 um surface
phyloseq-class experiment-level object
otu_table()   OTU Table:         [ 196 taxa and 17 samples ]
sample_data() Sample Data:       [ 17 samples by 61 sample variables ]
tax_table()   Taxonomy Table:    [ 196 taxa by 8 taxonomic ranks ]
============================
Phyloseq - 18S filter 3 um surface
phyloseq-class experiment-level object
otu_table()   OTU Table:         [ 229 taxa and 18 samples ]
sample_data() Sample Data:       [ 18 samples by 61 sample variables ]
tax_table()   Taxonomy Table:    [ 229 taxa by 8 taxonomic ranks ]
============================
Phyloseq - 18S filter 20 um surface
phyloseq-class experiment-level object
otu_table()   OTU Table:         [ 201 taxa and 15 samples ]
sample_data() Sample Data:       [ 15 samples by 61 sample variables ]
tax_table()   Taxonomy Table:    [ 201 taxa by 8 taxonomic ranks ]
============================
Phyloseq - 16S plastid 0.2 um surface
phyloseq-class experiment-level object
otu_table()   OTU Table:         [ 112 taxa and 11 samples ]
sample_data() Sample Data:       [ 11 samples by 61 sample variables ]
tax_table()   Taxonomy Table:    [ 112 taxa by 8 taxonomic ranks ]
============================
Phyloseq - 16S plastid 3 um surface
phyloseq-class experiment-level object
otu_table()   OTU Table:         [ 142 taxa and 16 samples ]
sample_data() Sample Data:       [ 16 samples by 61 sample variables ]
tax_table()   Taxonomy Table:    [ 142 taxa by 8 taxonomic ranks ]
============================
Phyloseq - 16S plastid 20 um surface
phyloseq-class experiment-level object
otu_table()   OTU Table:         [ 120 taxa and 13 samples ]
sample_data() Sample Data:       [ 13 samples by 61 sample variables ]
tax_table()   Taxonomy Table:    [ 120 taxa by 8 taxonomic ranks ]
============================
Phyloseq - 18S sort pico surface
phyloseq-class experiment-level object
otu_table()   OTU Table:         [ 65 taxa and 8 samples ]
sample_data() Sample Data:       [ 8 samples by 61 sample variables ]
tax_table()   Taxonomy Table:    [ 65 taxa by 8 taxonomic ranks ]
============================
Phyloseq - 18S sort nano surface
phyloseq-class experiment-level object
otu_table()   OTU Table:         [ 70 taxa and 8 samples ]
sample_data() Sample Data:       [ 8 samples by 61 sample variables ]
tax_table()   Taxonomy Table:    [ 70 taxa by 8 taxonomic ranks ]
============================

Normalize and transform to long form

18S filter surface
============================
========== 
phyloseq-class experiment-level object
otu_table()   OTU Table:         [ 394 taxa and 50 samples ]
sample_data() Sample Data:       [ 50 samples by 61 sample variables ]
tax_table()   Taxonomy Table:    [ 394 taxa by 8 taxonomic ranks ]

==========
The median number of reads used for normalization is  23202
16S plastid surface
============================
========== 
phyloseq-class experiment-level object
otu_table()   OTU Table:         [ 236 taxa and 40 samples ]
sample_data() Sample Data:       [ 40 samples by 61 sample variables ]
tax_table()   Taxonomy Table:    [ 236 taxa by 8 taxonomic ranks ]

==========
The median number of reads used for normalization is  28885
18S sort surface
============================
========== 
phyloseq-class experiment-level object
otu_table()   OTU Table:         [ 114 taxa and 16 samples ]
sample_data() Sample Data:       [ 16 samples by 61 sample variables ]
tax_table()   Taxonomy Table:    [ 114 taxa by 8 taxonomic ranks ]

==========
The median number of reads used for normalization is  27275
18S filter 0.2 um surface
============================
========== 
phyloseq-class experiment-level object
otu_table()   OTU Table:         [ 196 taxa and 17 samples ]
sample_data() Sample Data:       [ 17 samples by 61 sample variables ]
tax_table()   Taxonomy Table:    [ 196 taxa by 8 taxonomic ranks ]

==========
The median number of reads used for normalization is  14647
18S filter 3 um surface
============================
========== 
phyloseq-class experiment-level object
otu_table()   OTU Table:         [ 229 taxa and 18 samples ]
sample_data() Sample Data:       [ 18 samples by 61 sample variables ]
tax_table()   Taxonomy Table:    [ 229 taxa by 8 taxonomic ranks ]

==========
The median number of reads used for normalization is  24783
18S filter 20 um surface
============================
========== 
phyloseq-class experiment-level object
otu_table()   OTU Table:         [ 201 taxa and 15 samples ]
sample_data() Sample Data:       [ 15 samples by 61 sample variables ]
tax_table()   Taxonomy Table:    [ 201 taxa by 8 taxonomic ranks ]

==========
The median number of reads used for normalization is  29427
16S plastid 0.2 um surface
============================
========== 
phyloseq-class experiment-level object
otu_table()   OTU Table:         [ 112 taxa and 11 samples ]
sample_data() Sample Data:       [ 11 samples by 61 sample variables ]
tax_table()   Taxonomy Table:    [ 112 taxa by 8 taxonomic ranks ]

==========
The median number of reads used for normalization is  28471
16S plastid 3 um surface
============================
========== 
phyloseq-class experiment-level object
otu_table()   OTU Table:         [ 142 taxa and 16 samples ]
sample_data() Sample Data:       [ 16 samples by 61 sample variables ]
tax_table()   Taxonomy Table:    [ 142 taxa by 8 taxonomic ranks ]

==========
The median number of reads used for normalization is  31801
16S plastid 20 um surface
============================
========== 
phyloseq-class experiment-level object
otu_table()   OTU Table:         [ 120 taxa and 13 samples ]
sample_data() Sample Data:       [ 13 samples by 61 sample variables ]
tax_table()   Taxonomy Table:    [ 120 taxa by 8 taxonomic ranks ]

==========
The median number of reads used for normalization is  25641
18S sort pico surface
============================
========== 
phyloseq-class experiment-level object
otu_table()   OTU Table:         [ 65 taxa and 8 samples ]
sample_data() Sample Data:       [ 8 samples by 61 sample variables ]
tax_table()   Taxonomy Table:    [ 65 taxa by 8 taxonomic ranks ]

==========
The median number of reads used for normalization is  33258
18S sort nano surface
============================
========== 
phyloseq-class experiment-level object
otu_table()   OTU Table:         [ 70 taxa and 8 samples ]
sample_data() Sample Data:       [ 8 samples by 61 sample variables ]
tax_table()   Taxonomy Table:    [ 70 taxa by 8 taxonomic ranks ]

==========
The median number of reads used for normalization is  21650

List of classes

division class
Chlorophyta Chlorophyceae
Chlorophyta Mamiellophyceae
Chlorophyta Palmophyllophyceae
Chlorophyta Prasino-Clade-V
Chlorophyta Pyramimonadophyceae
Chlorophyta Trebouxiophyceae
Chlorophyta Ulvophyceae
Cryptophyta Cryptophyceae
Haptophyta Prymnesiophyceae
Ochrophyta Bacillariophyta
Ochrophyta Bolidophyceae
Ochrophyta Chrysophyceae
Ochrophyta Dictyochophyceae
Ochrophyta MOCH-1
Ochrophyta MOCH-2
Ochrophyta Pelagophyceae
Ochrophyta Phaeophyceae
Ochrophyta Xanthophyceae
Rhodophyta Bangiophyceae
Rhodophyta Florideophyceae

Heatmaps

Filter : Dictyo / Chrysophyceae /Pelago /Bacili / Crypto / Pyrami / Mamiello

Class

Most abundant 10%


========== 
phyloseq-class experiment-level object
otu_table()   OTU Table:         [ 7 taxa and 17 samples ]
sample_data() Sample Data:       [ 17 samples by 61 sample variables ]
tax_table()   Taxonomy Table:    [ 7 taxa by 8 taxonomic ranks ]

==========
The median number of reads used for normalization is  13808


========== 
phyloseq-class experiment-level object
otu_table()   OTU Table:         [ 7 taxa and 18 samples ]
sample_data() Sample Data:       [ 18 samples by 61 sample variables ]
tax_table()   Taxonomy Table:    [ 7 taxa by 8 taxonomic ranks ]

==========
The median number of reads used for normalization is  23366


========== 
phyloseq-class experiment-level object
otu_table()   OTU Table:         [ 5 taxa and 15 samples ]
sample_data() Sample Data:       [ 15 samples by 61 sample variables ]
tax_table()   Taxonomy Table:    [ 5 taxa by 8 taxonomic ranks ]

==========
The median number of reads used for normalization is  27860


========== 
phyloseq-class experiment-level object
otu_table()   OTU Table:         [ 4 taxa and 11 samples ]
sample_data() Sample Data:       [ 11 samples by 61 sample variables ]
tax_table()   Taxonomy Table:    [ 4 taxa by 8 taxonomic ranks ]

==========
The median number of reads used for normalization is  27592


========== 
phyloseq-class experiment-level object
otu_table()   OTU Table:         [ 5 taxa and 16 samples ]
sample_data() Sample Data:       [ 16 samples by 61 sample variables ]
tax_table()   Taxonomy Table:    [ 5 taxa by 8 taxonomic ranks ]

==========
The median number of reads used for normalization is  31460


========== 
phyloseq-class experiment-level object
otu_table()   OTU Table:         [ 4 taxa and 13 samples ]
sample_data() Sample Data:       [ 13 samples by 61 sample variables ]
tax_table()   Taxonomy Table:    [ 4 taxa by 8 taxonomic ranks ]

==========
The median number of reads used for normalization is  24881


========== 
phyloseq-class experiment-level object
otu_table()   OTU Table:         [ 4 taxa and 8 samples ]
sample_data() Sample Data:       [ 8 samples by 61 sample variables ]
tax_table()   Taxonomy Table:    [ 4 taxa by 8 taxonomic ranks ]

==========
The median number of reads used for normalization is  32016


========== 
phyloseq-class experiment-level object
otu_table()   OTU Table:         [ 4 taxa and 8 samples ]
sample_data() Sample Data:       [ 8 samples by 61 sample variables ]
tax_table()   Taxonomy Table:    [ 4 taxa by 8 taxonomic ranks ]

==========
The median number of reads used for normalization is  21054

Selected

class_selected <- c("Dictyochophyceae", "Chrysophyceae", "Pelagophyceae", "Bacillariophyta", 
    "Cryptophyceae", "Pyramimonadales", "Mamiellophyceae")

heatmap_class_selected <- list()

for (one_sample_type in sample_type_surface[4:11]) {
    
    reads_max <- case_when(str_detect(one_sample_type, "18S filter") ~ 30000, 
        str_detect(one_sample_type, "16S plastid") ~ 30000, str_detect(one_sample_type, 
            "18S sort") ~ 25000)
    
    ps_heat <- tax_glom(ps[[one_sample_type]], taxrank = "class") %>% subset_taxa(class %in% 
        class_selected)
    
    # Try to order by division and class...  tax_table <-
    # data.frame(tax_table(ps_heat)@.Data) taxa_names(ps_heat) <-
    # str_c(tax_table$division, tax_table$class, sep=' - ')
    
    gg <- plot_heatmap(ps_heat, method = "NMDS", distance = "bray", taxa.label = "class", 
        taxa.order = "class", sample.label = "sample_label", sample.order = "sample_label", 
        low = "beige", high = "red", na.value = "gray95", trans = NULL, title = one_sample_type) + 
        xlab("") + ylab("") + theme(axis.text.x = element_text(angle = 45, hjust = 1, 
        vjust = 1)) + scale_fill_gradient(limits = c(0, reads_max), low = "beige", 
        high = "red", na.value = "gray95")
    
    if (str_detect(one_sample_type, "18S filter 0.2")) 
        gg <- gg + geom_vline(xintercept = c(6.5, 9.5, 12.5))
    
    if (one_sample_type == "18S filter 3 um surface") 
        gg <- gg + geom_vline(xintercept = c(8.5, 10.5, 13.5))
    
    if (one_sample_type == "18S filter 20 um surface") 
        gg <- gg + geom_vline(xintercept = c(8.5, 9.5))
    
    
    # plot(heatmap(otu_table(ps_heat))) , trans = scales::log_trans(10)
    
    print(gg)
    
    heatmap_class_selected[[one_sample_type]] <- gg
    
}

Species

Most abundant


========== 
phyloseq-class experiment-level object
otu_table()   OTU Table:         [ 11 taxa and 17 samples ]
sample_data() Sample Data:       [ 17 samples by 61 sample variables ]
tax_table()   Taxonomy Table:    [ 11 taxa by 8 taxonomic ranks ]

==========
The median number of reads used for normalization is  11704


========== 
phyloseq-class experiment-level object
otu_table()   OTU Table:         [ 8 taxa and 18 samples ]
sample_data() Sample Data:       [ 18 samples by 61 sample variables ]
tax_table()   Taxonomy Table:    [ 8 taxa by 8 taxonomic ranks ]

==========
The median number of reads used for normalization is  20196


========== 
phyloseq-class experiment-level object
otu_table()   OTU Table:         [ 11 taxa and 15 samples ]
sample_data() Sample Data:       [ 15 samples by 61 sample variables ]
tax_table()   Taxonomy Table:    [ 11 taxa by 8 taxonomic ranks ]

==========
The median number of reads used for normalization is  26302


========== 
phyloseq-class experiment-level object
otu_table()   OTU Table:         [ 5 taxa and 11 samples ]
sample_data() Sample Data:       [ 11 samples by 61 sample variables ]
tax_table()   Taxonomy Table:    [ 5 taxa by 8 taxonomic ranks ]

==========
The median number of reads used for normalization is  27286


========== 
phyloseq-class experiment-level object
otu_table()   OTU Table:         [ 8 taxa and 16 samples ]
sample_data() Sample Data:       [ 16 samples by 61 sample variables ]
tax_table()   Taxonomy Table:    [ 8 taxa by 8 taxonomic ranks ]

==========
The median number of reads used for normalization is  30697


========== 
phyloseq-class experiment-level object
otu_table()   OTU Table:         [ 6 taxa and 13 samples ]
sample_data() Sample Data:       [ 13 samples by 61 sample variables ]
tax_table()   Taxonomy Table:    [ 6 taxa by 8 taxonomic ranks ]

==========
The median number of reads used for normalization is  24093


========== 
phyloseq-class experiment-level object
otu_table()   OTU Table:         [ 5 taxa and 8 samples ]
sample_data() Sample Data:       [ 8 samples by 61 sample variables ]
tax_table()   Taxonomy Table:    [ 5 taxa by 8 taxonomic ranks ]

==========
The median number of reads used for normalization is  28373


========== 
phyloseq-class experiment-level object
otu_table()   OTU Table:         [ 6 taxa and 8 samples ]
sample_data() Sample Data:       [ 8 samples by 61 sample variables ]
tax_table()   Taxonomy Table:    [ 6 taxa by 8 taxonomic ranks ]

==========
The median number of reads used for normalization is  19513

Selected

species_selected <- c("Thalassiosira_minima", "Fragilariopsis_cylindrus", "Minidiscus_sp.", 
    "Chaetoceros_neogracilis", "Porosira_glacialis", "Coretrhon_inerme", "Palmaria_palmata", 
    "Pseudo-nitzchia_seriata", "Micromonas_polaris", "Micromonas_clade_B3", 
    "Bathycoccus_prasinos", "Pyramimonas_gelidicola", "Geminigera_cryophila", 
    "Pelagophyceae_XXX_sp.", "Phaeocystis_antarctica")


heatmap_species_selected <- list()

for (one_sample_type in sample_type_surface[4:11]) {
    
    reads_max <- case_when(str_detect(one_sample_type, "18S filter") ~ 20000, 
        str_detect(one_sample_type, "16S plastid") ~ 5000, str_detect(one_sample_type, 
            "18S sort") ~ 15000)
    ps_heat <- tax_glom(ps[[one_sample_type]], taxrank = "species") %>% subset_taxa(species %in% 
        species_selected)
    
    # Try to order by division and species...  tax_table <-
    # data.frame(tax_table(ps_heat)@.Data) taxa_names(ps_heat) <-
    # str_c(tax_table$division, tax_table$species, sep=' - ')
    
    gg <- plot_heatmap(ps_heat, method = "NMDS", distance = "bray", taxa.label = "species", 
        taxa.order = "class", sample.label = "sample_label", sample.order = "sample_label", 
        low = "beige", high = "red", na.value = "gray95", trans = NULL, title = one_sample_type) + 
        xlab("") + ylab("") + theme(axis.text.x = element_text(angle = 45, hjust = 1, 
        vjust = 1)) + scale_fill_gradient(limits = c(0, reads_max), low = "beige", 
        high = "red", na.value = "gray95")
    
    if (str_detect(one_sample_type, "18S filter 0.2")) 
        gg <- gg + geom_vline(xintercept = c(6.5, 9.5, 12.5))
    
    if (one_sample_type == "18S filter 3 um surface") 
        gg <- gg + geom_vline(xintercept = c(8.5, 10.5, 13.5))
    
    if (one_sample_type == "18S filter 20 um surface") 
        gg <- gg + geom_vline(xintercept = c(8.5, 9.5))
    
    
    
    # plot(heatmap(otu_table(ps_heat))) , trans = scales::log_trans(10)
    
    print(gg)
    
    heatmap_species_selected[[one_sample_type]] <- gg
    
}

NMDS

Apply to all samples

Square root transformation
Wisconsin double standardization
Run 0 stress 0.1687566 
Run 1 stress 0.1687634 
... Procrustes: rmse 0.002985303  max resid 0.01690689 
Run 2 stress 0.1687197 
... New best solution
... Procrustes: rmse 0.002431247  max resid 0.01134347 
Run 3 stress 0.1733998 
Run 4 stress 0.1739068 
Run 5 stress 0.1766939 
Run 6 stress 0.1687159 
... New best solution
... Procrustes: rmse 0.001111716  max resid 0.005731252 
... Similar to previous best
Run 7 stress 0.1733984 
Run 8 stress 0.1739071 
Run 9 stress 0.1746154 
Run 10 stress 0.1835842 
Run 11 stress 0.168719 
... Procrustes: rmse 0.001095126  max resid 0.005701493 
... Similar to previous best
Run 12 stress 0.1835529 
Run 13 stress 0.168719 
... Procrustes: rmse 0.001110988  max resid 0.005739634 
... Similar to previous best
Run 14 stress 0.168719 
... Procrustes: rmse 0.001112726  max resid 0.005733226 
... Similar to previous best
Run 15 stress 0.1733994 
Run 16 stress 0.1745761 
Run 17 stress 0.1721531 
Run 18 stress 0.1734118 
Run 19 stress 0.1872138 
Run 20 stress 0.1687632 
... Procrustes: rmse 0.003837324  max resid 0.01748068 
*** Solution reached
[1] 3

Call:
metaMDS(comm = veganifyOTU(physeq), distance = distance) 

global Multidimensional Scaling using monoMDS

Data:     wisconsin(sqrt(veganifyOTU(physeq))) 
Distance: bray 

Dimensions: 2 
Stress:     0.1687159 
Stress type 1, weak ties
Two convergent solutions found after 20 tries
Scaling: centring, PC rotation, halfchange scaling 
Species: expanded scores based on 'wisconsin(sqrt(veganifyOTU(physeq)))' 

Square root transformation
Wisconsin double standardization
Run 0 stress 0.1492484 
Run 1 stress 0.1492468 
... New best solution
... Procrustes: rmse 0.0002507616  max resid 0.001358323 
... Similar to previous best
Run 2 stress 0.1489429 
... New best solution
... Procrustes: rmse 0.01404688  max resid 0.06477591 
Run 3 stress 0.1732926 
Run 4 stress 0.1489447 
... Procrustes: rmse 0.0005970766  max resid 0.003273668 
... Similar to previous best
Run 5 stress 0.1526353 
Run 6 stress 0.1489494 
... Procrustes: rmse 0.001870841  max resid 0.01026137 
Run 7 stress 0.1489076 
... New best solution
... Procrustes: rmse 0.005462155  max resid 0.02114027 
Run 8 stress 0.1489094 
... Procrustes: rmse 0.0002241435  max resid 0.00122347 
... Similar to previous best
Run 9 stress 0.1931313 
Run 10 stress 0.1526371 
Run 11 stress 0.1669089 
Run 12 stress 0.2018991 
Run 13 stress 0.188055 
Run 14 stress 0.1526361 
Run 15 stress 0.1547389 
Run 16 stress 0.1760578 
Run 17 stress 0.1762028 
Run 18 stress 0.1965688 
Run 19 stress 0.1755688 
Run 20 stress 0.1870225 
*** Solution reached
[1] 3

Call:
metaMDS(comm = veganifyOTU(physeq), distance = distance) 

global Multidimensional Scaling using monoMDS

Data:     wisconsin(sqrt(veganifyOTU(physeq))) 
Distance: bray 

Dimensions: 2 
Stress:     0.1489076 
Stress type 1, weak ties
Two convergent solutions found after 20 tries
Scaling: centring, PC rotation, halfchange scaling 
Species: expanded scores based on 'wisconsin(sqrt(veganifyOTU(physeq)))' 

Square root transformation
Wisconsin double standardization
Run 0 stress 0.05090316 
Run 1 stress 0.05736207 
Run 2 stress 0.05090323 
... Procrustes: rmse 0.0001234125  max resid 0.0002263345 
... Similar to previous best
Run 3 stress 0.05185334 
Run 4 stress 0.05090317 
... Procrustes: rmse 3.166825e-05  max resid 5.733514e-05 
... Similar to previous best
Run 5 stress 0.05090316 
... Procrustes: rmse 3.131882e-05  max resid 5.132691e-05 
... Similar to previous best
Run 6 stress 0.05161249 
Run 7 stress 0.0520288 
Run 8 stress 0.05379784 
Run 9 stress 0.05723174 
Run 10 stress 0.05161249 
Run 11 stress 0.05379785 
Run 12 stress 0.05220006 
Run 13 stress 0.05940653 
Run 14 stress 0.05533946 
Run 15 stress 0.05344022 
Run 16 stress 0.05220002 
Run 17 stress 0.05161251 
Run 18 stress 0.05379788 
Run 19 stress 0.05161248 
Run 20 stress 0.0520288 
*** Solution reached
[1] 3

Call:
metaMDS(comm = veganifyOTU(physeq), distance = distance) 

global Multidimensional Scaling using monoMDS

Data:     wisconsin(sqrt(veganifyOTU(physeq))) 
Distance: bray 

Dimensions: 2 
Stress:     0.05090316 
Stress type 1, weak ties
Two convergent solutions found after 20 tries
Scaling: centring, PC rotation, halfchange scaling 
Species: expanded scores based on 'wisconsin(sqrt(veganifyOTU(physeq)))' 

Vertical profile

  • Station 6 - 2015-01-16
  • Very important, must remove taxa that are not present in the filtered samples
  • Do not use the TFF

Filter the data


========== 
phyloseq-class experiment-level object
otu_table()   OTU Table:         [ 175 taxa and 15 samples ]
sample_data() Sample Data:       [ 15 samples by 61 sample variables ]
tax_table()   Taxonomy Table:    [ 175 taxa by 8 taxonomic ranks ]

==========
The median number of reads used for normalization is  43491Phyloseq - 18S filter profile
phyloseq-class experiment-level object
otu_table()   OTU Table:         [ 175 taxa and 15 samples ]
sample_data() Sample Data:       [ 15 samples by 61 sample variables ]
tax_table()   Taxonomy Table:    [ 175 taxa by 8 taxonomic ranks ]
============================

========== 
phyloseq-class experiment-level object
otu_table()   OTU Table:         [ 107 taxa and 15 samples ]
sample_data() Sample Data:       [ 15 samples by 61 sample variables ]
tax_table()   Taxonomy Table:    [ 107 taxa by 8 taxonomic ranks ]

==========
The median number of reads used for normalization is  41130Phyloseq - 16S plastid profile
phyloseq-class experiment-level object
otu_table()   OTU Table:         [ 107 taxa and 15 samples ]
sample_data() Sample Data:       [ 15 samples by 61 sample variables ]
tax_table()   Taxonomy Table:    [ 107 taxa by 8 taxonomic ranks ]
============================

========== 
phyloseq-class experiment-level object
otu_table()   OTU Table:         [ 96 taxa and 10 samples ]
sample_data() Sample Data:       [ 10 samples by 61 sample variables ]
tax_table()   Taxonomy Table:    [ 96 taxa by 8 taxonomic ranks ]

==========
The median number of reads used for normalization is  29305Phyloseq - 18S sort profile
phyloseq-class experiment-level object
otu_table()   OTU Table:         [ 96 taxa and 10 samples ]
sample_data() Sample Data:       [ 10 samples by 61 sample variables ]
tax_table()   Taxonomy Table:    [ 96 taxa by 8 taxonomic ranks ]
============================

========== 
phyloseq-class experiment-level object
otu_table()   OTU Table:         [ 92 taxa and 5 samples ]
sample_data() Sample Data:       [ 5 samples by 61 sample variables ]
tax_table()   Taxonomy Table:    [ 92 taxa by 8 taxonomic ranks ]

==========
The median number of reads used for normalization is  30265Phyloseq - 18S filter 0.2 um profile
phyloseq-class experiment-level object
otu_table()   OTU Table:         [ 92 taxa and 5 samples ]
sample_data() Sample Data:       [ 5 samples by 61 sample variables ]
tax_table()   Taxonomy Table:    [ 92 taxa by 8 taxonomic ranks ]
============================

========== 
phyloseq-class experiment-level object
otu_table()   OTU Table:         [ 86 taxa and 5 samples ]
sample_data() Sample Data:       [ 5 samples by 61 sample variables ]
tax_table()   Taxonomy Table:    [ 86 taxa by 8 taxonomic ranks ]

==========
The median number of reads used for normalization is  31205Phyloseq - 18S filter 3 um profile
phyloseq-class experiment-level object
otu_table()   OTU Table:         [ 86 taxa and 5 samples ]
sample_data() Sample Data:       [ 5 samples by 61 sample variables ]
tax_table()   Taxonomy Table:    [ 86 taxa by 8 taxonomic ranks ]
============================

========== 
phyloseq-class experiment-level object
otu_table()   OTU Table:         [ 121 taxa and 5 samples ]
sample_data() Sample Data:       [ 5 samples by 61 sample variables ]
tax_table()   Taxonomy Table:    [ 121 taxa by 8 taxonomic ranks ]

==========
The median number of reads used for normalization is  58797Phyloseq - 18S filter 20 um profile
phyloseq-class experiment-level object
otu_table()   OTU Table:         [ 121 taxa and 5 samples ]
sample_data() Sample Data:       [ 5 samples by 61 sample variables ]
tax_table()   Taxonomy Table:    [ 121 taxa by 8 taxonomic ranks ]
============================

========== 
phyloseq-class experiment-level object
otu_table()   OTU Table:         [ 46 taxa and 5 samples ]
sample_data() Sample Data:       [ 5 samples by 61 sample variables ]
tax_table()   Taxonomy Table:    [ 46 taxa by 8 taxonomic ranks ]

==========
The median number of reads used for normalization is  40267Phyloseq - 16S plastid 0.2 um profile
phyloseq-class experiment-level object
otu_table()   OTU Table:         [ 46 taxa and 5 samples ]
sample_data() Sample Data:       [ 5 samples by 61 sample variables ]
tax_table()   Taxonomy Table:    [ 46 taxa by 8 taxonomic ranks ]
============================

========== 
phyloseq-class experiment-level object
otu_table()   OTU Table:         [ 62 taxa and 5 samples ]
sample_data() Sample Data:       [ 5 samples by 61 sample variables ]
tax_table()   Taxonomy Table:    [ 62 taxa by 8 taxonomic ranks ]

==========
The median number of reads used for normalization is  46172Phyloseq - 16S plastid 3 um profile
phyloseq-class experiment-level object
otu_table()   OTU Table:         [ 62 taxa and 5 samples ]
sample_data() Sample Data:       [ 5 samples by 61 sample variables ]
tax_table()   Taxonomy Table:    [ 62 taxa by 8 taxonomic ranks ]
============================

========== 
phyloseq-class experiment-level object
otu_table()   OTU Table:         [ 74 taxa and 5 samples ]
sample_data() Sample Data:       [ 5 samples by 61 sample variables ]
tax_table()   Taxonomy Table:    [ 74 taxa by 8 taxonomic ranks ]

==========
The median number of reads used for normalization is  47020Phyloseq - 16S plastid 20 um profile
phyloseq-class experiment-level object
otu_table()   OTU Table:         [ 74 taxa and 5 samples ]
sample_data() Sample Data:       [ 5 samples by 61 sample variables ]
tax_table()   Taxonomy Table:    [ 74 taxa by 8 taxonomic ranks ]
============================

========== 
phyloseq-class experiment-level object
otu_table()   OTU Table:         [ 65 taxa and 5 samples ]
sample_data() Sample Data:       [ 5 samples by 61 sample variables ]
tax_table()   Taxonomy Table:    [ 65 taxa by 8 taxonomic ranks ]

==========
The median number of reads used for normalization is  29412Phyloseq - 18S sort pico profile
phyloseq-class experiment-level object
otu_table()   OTU Table:         [ 65 taxa and 5 samples ]
sample_data() Sample Data:       [ 5 samples by 61 sample variables ]
tax_table()   Taxonomy Table:    [ 65 taxa by 8 taxonomic ranks ]
============================

========== 
phyloseq-class experiment-level object
otu_table()   OTU Table:         [ 46 taxa and 5 samples ]
sample_data() Sample Data:       [ 5 samples by 61 sample variables ]
tax_table()   Taxonomy Table:    [ 46 taxa by 8 taxonomic ranks ]

==========
The median number of reads used for normalization is  28502Phyloseq - 18S sort nano profile
phyloseq-class experiment-level object
otu_table()   OTU Table:         [ 46 taxa and 5 samples ]
sample_data() Sample Data:       [ 5 samples by 61 sample variables ]
tax_table()   Taxonomy Table:    [ 46 taxa by 8 taxonomic ranks ]
============================

Compare the contributions of CLASS and SPECIS using the different methods

Sample by sample comparison

  • Each dot corresponds to the relative contribution of the taxonomic level considered for a sample for which both 18S and 16S has been performed

Global comparison of species found with the 3 methods

  • Compute table of number of samples for each species (rows) vs the three methods (columns)

  • Only keep

    • 2015 samples because it is the only dataset for which we have the three types of samples
    • 0.2 and 3 um fractions (to be comparable with sorting)
  • Remove species that contains _X

Class not found in one type of sample
18S filter
division class n_reads_18S_filter n_samples_18S_filter n_reads_16S_plastid n_samples_16S_plastid n_reads_18S_sort n_samples_18S_sort
Chlorophyta Prasino-Clade-V NA NA 0.404492 29 NA NA
18S sort
division class n_reads_18S_filter n_samples_18S_filter n_reads_16S_plastid n_samples_16S_plastid n_reads_18S_sort n_samples_18S_sort
Chlorophyta Trebouxiophyceae 0.0004002 3 0.0004331 3 NA NA
Rhodophyta Florideophyceae 0.0755969 29 0.0018921 10 NA NA
Chlorophyta Prasino-Clade-V NA NA 0.4044920 29 NA NA
16S filter
division class n_reads_18S_filter n_samples_18S_filter n_reads_16S_plastid n_samples_16S_plastid n_reads_18S_sort n_samples_18S_sort
Chlorophyta Ulvophyceae 0.0258306 24 NA NA 0.5714412 4
Ochrophyta MOCH-2 0.0334232 28 NA NA 0.0449041 11
Species  found in the three types of samples
18S filter
division class order family genus species n_reads_18S_filter n_samples_18S_filter n_reads_16S_plastid n_samples_16S_plastid n_reads_18S_sort n_samples_18S_sort
Chlorophyta Mamiellophyceae Mamiellales Bathycoccaceae Bathycoccus Bathycoccus_prasinos 0.2422204 32 0.0038980 3 1.1036274 23
Chlorophyta Mamiellophyceae Mamiellales Mamiellaceae Mantoniella Mantoniella_squamata 0.0004829 1 0.0559522 24 0.0013399 1
Cryptophyta Cryptophyceae Cryptomonadales Cryptomonadales_X Geminigera Geminigera_cryophila 8.7159220 35 0.0000594 1 5.9759821 30
Haptophyta Prymnesiophyceae Phaeocystales Phaeocystaceae Phaeocystis Phaeocystis_antarctica 0.9069443 35 0.0297455 10 11.2070634 42
Haptophyta Prymnesiophyceae Phaeocystales Phaeocystaceae Phaeocystis Phaeocystis_sp. 0.0004760 1 7.1265134 30 0.1486057 14
Ochrophyta Bacillariophyta Bacillariophyta_X Polar-centric-Mediophyceae Thalassiosira Thalassiosira_sp. 1.4038636 34 4.1583544 30 0.8233117 16
Ochrophyta Bacillariophyta Bacillariophyta_X Raphid-pennate Fragilariopsis Fragilariopsis_cylindrus 4.2004487 35 1.1061643 30 6.6987788 42
Ochrophyta Dictyochophyceae Dictyochophyceae_X Florenciellales Florenciella Florenciella_parvula 0.0539616 30 0.0021032 4 0.0109493 9
Ochrophyta Phaeophyceae Phaeophyceae_X Phaeophyceae_XX Ectocarpus Ectocarpus_siliculosus 0.0193789 1 0.0004854 2 0.0031598 2
Species only found in one type of sample
18S filter
division class order family genus species n_reads_18S_filter n_samples_18S_filter n_reads_16S_plastid n_samples_16S_plastid n_reads_18S_sort n_samples_18S_sort
Chlorophyta Chlorophyceae Chaetopeltidales Chaetopeltidaceae Planophila Planophila_sp. 0.0003221 1 NA NA NA NA
Chlorophyta Chlorophyceae Chlamydomonadales Chlamydomonadales_X Chlamydomonas Chlamydomonas_acidophila 0.0001343 1 NA NA NA NA
Chlorophyta Chlorophyceae Chlamydomonadales Chlamydomonadales_X Chlamydomonas Chlamydomonas_hedleyi 0.0006203 2 NA NA NA NA
Chlorophyta Chlorophyceae Chlamydomonadales Chlamydomonadales_X Chlamydomonas Chlamydomonas_kuwadae 0.0013583 6 NA NA NA NA
Chlorophyta Chlorophyceae Chlamydomonadales Chlamydomonadales_X Haematococcus Haematococcus_zimbabwiensis 0.0001602 1 NA NA NA NA
Chlorophyta Chlorophyceae Chlamydomonadales Chlamydomonadales_X Pleurastrum Pleurastrum_sp. 0.0009742 3 NA NA NA NA
Chlorophyta Trebouxiophyceae Prasiolales Prasiolales_X Desmococcus Desmococcus_endolithicus 0.0000585 1 NA NA NA NA
Chlorophyta Trebouxiophyceae Watanabea-Clade Watanabea-Clade_X Chloroidium Chloroidium_ellipsoideum 0.0001530 1 NA NA NA NA
Chlorophyta Ulvophyceae Ulotrichales Ulotrichales_X Chlorothrix Chlorothrix_sp. 0.0018758 2 NA NA NA NA
Chlorophyta Ulvophyceae Ulvales-relatives Ulvales-relatives_X Dilabifilum Dilabifilum_sp. 0.0002731 1 NA NA NA NA
Cryptophyta Cryptophyceae Cryptomonadales Cryptomonadales_X Falcomonas Falcomonas_sp. 0.0002160 2 NA NA NA NA
Cryptophyta Cryptophyceae Cryptomonadales Cryptomonadales_X Hemiselmis Hemiselmis_tepida 0.0061589 7 NA NA NA NA
Ochrophyta Bacillariophyta Bacillariophyta_X Araphid-pennate Grammonema Grammonema_striatula 0.0003498 3 NA NA NA NA
Ochrophyta Bacillariophyta Bacillariophyta_X Araphid-pennate Licmophora Licmophora_grandis 0.0007432 1 NA NA NA NA
Ochrophyta Bacillariophyta Bacillariophyta_X Araphid-pennate Pteroncola Pteroncola_inane 0.0007406 4 NA NA NA NA
Ochrophyta Bacillariophyta Bacillariophyta_X Araphid-pennate Thalassionema Thalassionema_frauenfeldii 0.0011473 2 NA NA NA NA
Ochrophyta Bacillariophyta Bacillariophyta_X Polar-centric-Mediophyceae Chaetoceros Chaetoceros_peruvianus 0.0003611 3 NA NA NA NA
Ochrophyta Bacillariophyta Bacillariophyta_X Polar-centric-Mediophyceae Eucampia Eucampia_antarctica 0.0005297 3 NA NA NA NA
Ochrophyta Bacillariophyta Bacillariophyta_X Polar-centric-Mediophyceae Hemiaulus Hemiaulus_sinensis 0.0001122 1 NA NA NA NA
Ochrophyta Bacillariophyta Bacillariophyta_X Polar-centric-Mediophyceae Minidiscus Minidiscus_trioculatus 0.0354069 7 NA NA NA NA
Ochrophyta Bacillariophyta Bacillariophyta_X Polar-centric-Mediophyceae Odontella Odontella_aurita 0.0000751 1 NA NA NA NA
Ochrophyta Bacillariophyta Bacillariophyta_X Polar-centric-Mediophyceae Porosira Porosira_pseudodelicatula 0.0003758 1 NA NA NA NA
Ochrophyta Bacillariophyta Bacillariophyta_X Polar-centric-Mediophyceae Shionodiscus Shionodiscus_ritscheri 0.0173100 2 NA NA NA NA
Ochrophyta Bacillariophyta Bacillariophyta_X Polar-centric-Mediophyceae Thalassiosira Thalassiosira_antarctica 0.0001088 1 NA NA NA NA
Ochrophyta Bacillariophyta Bacillariophyta_X Polar-centric-Mediophyceae Thalassiosira Thalassiosira_minuscula 0.0000748 1 NA NA NA NA
Ochrophyta Bacillariophyta Bacillariophyta_X Polar-centric-Mediophyceae Thalassiosira Thalassiosira_tumida 0.0007959 1 NA NA NA NA
Ochrophyta Bacillariophyta Bacillariophyta_X Radial-centric-basal-Coscinodiscophyceae Actinocyclus Actinocyclus_actinochilus 0.0017113 4 NA NA NA NA
Ochrophyta Bacillariophyta Bacillariophyta_X Radial-centric-basal-Coscinodiscophyceae Rhizosolenia Rhizosolenia_fallax 0.0000685 1 NA NA NA NA
Ochrophyta Bacillariophyta Bacillariophyta_X Radial-centric-basal-Coscinodiscophyceae Stellarima Stellarima_microtrias 0.0001769 1 NA NA NA NA
Ochrophyta Bacillariophyta Bacillariophyta_X Raphid-pennate Amphora Amphora_proteus 0.0057413 2 NA NA NA NA
Ochrophyta Bacillariophyta Bacillariophyta_X Raphid-pennate Cylindrotheca Cylindrotheca_closterium 0.0002630 1 NA NA NA NA
Ochrophyta Bacillariophyta Bacillariophyta_X Raphid-pennate Cymbella Cymbella_gastroides 0.0041439 12 NA NA NA NA
Ochrophyta Bacillariophyta Bacillariophyta_X Raphid-pennate Encyonema Encyonema_sp. 0.0016080 7 NA NA NA NA
Ochrophyta Bacillariophyta Bacillariophyta_X Raphid-pennate Haslea Haslea_spicula 0.0011842 4 NA NA NA NA
Ochrophyta Bacillariophyta Bacillariophyta_X Raphid-pennate Navicula Navicula_perminuta 0.0000805 1 NA NA NA NA
Ochrophyta Bacillariophyta Bacillariophyta_X Raphid-pennate Navicula Navicula_sp. 0.0008106 3 NA NA NA NA
Ochrophyta Bacillariophyta Bacillariophyta_X Raphid-pennate Nitzschia Nitzschia_dissipata 0.0001239 1 NA NA NA NA
Ochrophyta Bacillariophyta Bacillariophyta_X Raphid-pennate Nitzschia Nitzschia_sp. 0.0001170 1 NA NA NA NA
Ochrophyta Bacillariophyta Bacillariophyta_X Raphid-pennate Pauliella Pauliella_toeniata 0.0002738 1 NA NA NA NA
Ochrophyta Bacillariophyta Bacillariophyta_X Raphid-pennate Pleurosigma Pleurosigma_intermedium 0.0011815 3 NA NA NA NA
Ochrophyta Bacillariophyta Bacillariophyta_X Raphid-pennate Pseudo-nitzschia Pseudo-nitzschia_turgidula 0.0001264 1 NA NA NA NA
Ochrophyta Bacillariophyta Bacillariophyta_X Raphid-pennate Pseudogomphonema Pseudogomphonema_sp. 0.0059704 11 NA NA NA NA
Ochrophyta Bolidophyceae Parmales Parmales_env_3 Parmales_env_3A Parmales_env_3A_sp. 0.0120071 10 NA NA NA NA
Ochrophyta Chrysophyceae Chrysophyceae_X Chrysophyceae_Clade-C Spumella Spumella_elongata 0.0144543 5 NA NA NA NA
Ochrophyta Chrysophyceae Chrysophyceae_X Chrysophyceae_Clade-F Paraphysomonas Paraphysomonas_imperforata 0.0026271 5 NA NA NA NA
Ochrophyta Dictyochophyceae Dictyochophyceae_X Pedinellales Pseudopedinella Pseudopedinella_sp. 0.0001042 1 NA NA NA NA
Ochrophyta Phaeophyceae Phaeophyceae_X Phaeophyceae_XX Pylaiella Pylaiella_littoralis 0.0005950 1 NA NA NA NA
Rhodophyta Florideophyceae Ceramiales Delesseriaceae Hemineura Hemineura_frondosa 0.0000743 1 NA NA NA NA
Rhodophyta Florideophyceae Ceramiales Delesseriaceae Phycodrys Phycodrys_rubens 0.0000850 1 NA NA NA NA
Rhodophyta Florideophyceae Corallinales Corallinales_X Hapalidiaceae Hapalidiaceae_sp. 0.0003964 1 NA NA NA NA
Rhodophyta Florideophyceae Corallinales Corallinales_X Mesophyllum Mesophyllum_sp. 0.0267372 24 NA NA NA NA
Rhodophyta Florideophyceae Corallinales Corallinales_X Synarthrophyton Synarthrophyton_patena 0.0007191 2 NA NA NA NA
Rhodophyta Florideophyceae Gigartinales Gigartinales_X Chondrus Chondrus_nipponicus 0.0420698 23 NA NA NA NA
Rhodophyta Florideophyceae Gigartinales Gigartinales_X Stenogramme Stenogramme_interrupta 0.0015735 2 NA NA NA NA
Rhodophyta Florideophyceae Gracilariales Gracilariales_X Curdiea Curdiea_codiodes 0.0011262 4 NA NA NA NA
Rhodophyta Florideophyceae Halymeniales Halymeniales_X Pachymenia Pachymenia_orbicularis 0.0000991 1 NA NA NA NA
Rhodophyta Florideophyceae Plocamiales Plocamiales_X Trematocarpus Trematocarpus_fragilis 0.0004336 2 NA NA NA NA
18S sort
division class order family genus species n_reads_18S_filter n_samples_18S_filter n_reads_16S_plastid n_samples_16S_plastid n_reads_18S_sort n_samples_18S_sort
Chlorophyta Ulvophyceae Ulotrichales Ulotrichales_X Ulothrix Ulothrix_zonata NA NA NA NA 0.0014895 1
Cryptophyta Cryptophyceae Cryptomonadales Cryptomonadales_X Falcomonas Falcomonas_daucoides NA NA NA NA 0.0026517 4
Cryptophyta Cryptophyceae Cryptomonadales Cryptomonadales_X Hemiselmis Hemiselmis_sp. NA NA NA NA 0.0001032 1
Haptophyta Prymnesiophyceae Phaeocystales Phaeocystaceae Phaeocystis Phaeocystis_pouchetii NA NA NA NA 0.0021350 3
Ochrophyta Bacillariophyta Bacillariophyta_X Polar-centric-Mediophyceae Bacterosira Bacterosira_sp. NA NA NA NA 0.0000804 1
Ochrophyta Bacillariophyta Bacillariophyta_X Polar-centric-Mediophyceae Skeletonema Skeletonema_sp. NA NA NA NA 0.0000463 1
Ochrophyta Bacillariophyta Bacillariophyta_X Raphid-pennate Bacillaria Bacillaria_paxillifer NA NA NA NA 0.0002977 1
Ochrophyta Bacillariophyta Bacillariophyta_X Raphid-pennate Luka_AeN707 Luka_AeN707-96_sp. NA NA NA NA 0.0016083 3
Ochrophyta Dictyochophyceae Dictyochophyceae_X Florenciellales Pseudochattonella Pseudochattonella_verruculosa NA NA NA NA 0.0012825 1
Ochrophyta Pelagophyceae Pelagomonadales Pelagomonadaceae Pelagomonadaceae_clade_A Pelagomonadaceae_clade_A_sp. NA NA NA NA 0.0010176 2
Ochrophyta Pelagophyceae Sarcinochrysidales Sarcinochrysidaceae Ankylochrysis Ankylochrysis_sp. NA NA NA NA 0.0000885 1
Ochrophyta Pelagophyceae Sarcinochrysidales Sarcinochrysidaceae Sarcinochrysis Sarcinochrysis_marina NA NA NA NA 0.0000491 1
16S filter
division class order family genus species n_reads_18S_filter n_samples_18S_filter n_reads_16S_plastid n_samples_16S_plastid n_reads_18S_sort n_samples_18S_sort
Chlorophyta Chlorophyceae Chlamydomonadales Chlamydomonadales_X Oophila Oophila_amblystomatis NA NA 0.0001469 2 NA NA
Chlorophyta Palmophyllophyceae Prasinococcales Prasinococcales-Clade-B Prasinoderma Prasinoderma_coloniale NA NA 0.0200905 24 NA NA
Chlorophyta Pyramimonadophyceae Pyramimonadales Pyramimonadaceae Pyramimonas Pyramimonas_disomata NA NA 0.0001915 2 NA NA
Chlorophyta Pyramimonadophyceae Pyramimonadales Pyramimonadaceae Pyramimonas Pyramimonas_sp. NA NA 4.9391166 30 NA NA
Chlorophyta Trebouxiophyceae Chlorellales Chlorellales_X Chlorella Chlorella_vulgaris NA NA 0.0001729 1 NA NA
Haptophyta Prymnesiophyceae Phaeocystales Phaeocystaceae Phaeocystis Phaeocystis_globosa NA NA 4.1611794 30 NA NA
Haptophyta Prymnesiophyceae Prymnesiales Prymnesiaceae Dicrateria Dicrateria_sp. NA NA 0.0064689 17 NA NA
Ochrophyta Bacillariophyta Bacillariophyta_X Araphid-pennate Grammonema Grammonema_striatulum NA NA 0.0003316 1 NA NA
Ochrophyta Bacillariophyta Bacillariophyta_X Polar-centric-Mediophyceae Chaetoceros Chaetoceros_sp. NA NA 0.1147767 26 NA NA
Ochrophyta Bacillariophyta Bacillariophyta_X Polar-centric-Mediophyceae Conticribra Conticribra_weissflogii NA NA 0.0001386 1 NA NA
Ochrophyta Bacillariophyta Bacillariophyta_X Polar-centric-Mediophyceae Lauderia Lauderia_annulata NA NA 0.0000594 1 NA NA
Ochrophyta Bacillariophyta Bacillariophyta_X Polar-centric-Mediophyceae Odontella Odontella_sinensis NA NA 0.1707281 25 NA NA
Ochrophyta Bacillariophyta Bacillariophyta_X Polar-centric-Mediophyceae Thalassiosira Thalassiosira_nordenskioeldii NA NA 0.0001708 1 NA NA
Ochrophyta Bacillariophyta Bacillariophyta_X Radial-centric-basal-Coscinodiscophyceae Corethron Corethron_pennatum NA NA 0.0290473 22 NA NA
Ochrophyta Bolidophyceae Parmales Triparmaceae Triparma Triparma_pacifica NA NA 0.0103977 5 NA NA
Ochrophyta Dictyochophyceae Dictyochophyceae_X Pedinellales Helicopedinella Helicopedinella_sp. NA NA 0.0073091 5 NA NA
Ochrophyta Dictyochophyceae Dictyochophyceae_X Pedinellales Mesopedinella Mesopedinella_arctica NA NA 0.0004326 3 NA NA
Ochrophyta Pelagophyceae Pelagomonadales Pelagomonadaceae Aureococcus Aureococcus_anophagefferens NA NA 0.4848461 30 NA NA
Rhodophyta Florideophyceae Ahnfeltiales Ahnfeltiaceae Ahnfeltia Ahnfeltia_plicata NA NA 0.0001100 1 NA NA
Rhodophyta Florideophyceae Gigartinales Gigartinales_X Chondrus Chondrus_crispus NA NA 0.0012824 8 NA NA

png 
  2 

Comparison of species found in the different fractions for 18S filter and 18S sorted

  • Compute table of number of samples for each species (rows) vs the three fractions (columns)

  • Only keep

    • 2015 samples because it is the only dataset for which we have the three types of samples
    • Genera that do not contain _X
division class > 20 um 0.2-3 um 3-20 um nano pico
Chlorophyta Chlorophyceae 7 5 5 1 NA
Chlorophyta Mamiellophyceae 17 18 17 18 22
Chlorophyta Palmophyllophyceae 4 15 16 1 1
Chlorophyta Pyramimonadophyceae 18 18 17 19 4
Chlorophyta Trebouxiophyceae 4 NA 3 NA NA
Chlorophyta Ulvophyceae 14 11 13 2 2
Cryptophyta Cryptophyceae 19 18 17 22 9
Haptophyta Prymnesiophyceae 19 18 17 22 22
Ochrophyta Bacillariophyta 19 18 17 22 22
Ochrophyta Bolidophyceae 19 18 17 21 20
Ochrophyta Chrysophyceae 14 17 17 2 2
Ochrophyta Dictyochophyceae 11 18 17 15 1
Ochrophyta MOCH-2 10 13 15 11 NA
Ochrophyta Pelagophyceae 19 18 17 22 22
Ochrophyta Phaeophyceae 19 12 17 10 NA
Rhodophyta Florideophyceae 18 13 16 NA NA
division class order family genus species > 20 um 0.2-3 um 3-20 um nano pico
Chlorophyta Chlorophyceae Chlamydomonadales Chlamydomonadales_X Chlamydomonas Chlamydomonas_kuwadae 5 3 3 NA NA
Chlorophyta Chlorophyceae Chlamydomonadales Chlamydomonadales_X Chlamydomonas Chlamydomonas_raudensis 1 NA 1 1 NA
Chlorophyta Chlorophyceae Chlamydomonadales Chlamydomonadales_X Pleurastrum Pleurastrum_sp. 1 1 2 NA NA
Chlorophyta Chlorophyceae Sphaeropleales Sphaeropleales_X Radiococcus Radiococcus_polycoccus 1 NA NA NA NA
Chlorophyta Mamiellophyceae Dolichomastigales Dolichomastigaceae Dolichomastigaceae-B Dolichomastigaceae-B_sp. 12 18 17 1 5
Chlorophyta Mamiellophyceae Mamiellales Bathycoccaceae Bathycoccus Bathycoccus_prasinos 5 17 15 1 22
Chlorophyta Mamiellophyceae Mamiellales Mamiellaceae Micromonas Micromonas_polaris 17 17 17 17 22
Chlorophyta Palmophyllophyceae Prasinococcales Prasinococcales-Clade-B Prasinoderma Prasinoderma_sp. 4 15 16 1 1
Chlorophyta Pyramimonadophyceae Pyramimonadales Pyramimonadaceae Pyramimonas Pyramimonas_australis 13 17 17 10 2
Chlorophyta Pyramimonadophyceae Pyramimonadales Pyramimonadaceae Pyramimonas Pyramimonas_gelidicola 18 18 17 19 4
Chlorophyta Trebouxiophyceae Chlorellales Chlorellales_X Chlorella Chlorella_sorokiniana 1 NA NA NA NA
Chlorophyta Ulvophyceae Ulotrichales Ulotrichales_X Chlorothrix Chlorothrix_sp. 4 NA 2 NA NA
Chlorophyta Ulvophyceae Ulotrichales Ulotrichales_X Monostroma Monostroma_grevillei 10 9 10 2 1
Chlorophyta Ulvophyceae Ulotrichales Ulotrichales_X Ulothrix Ulothrix_zonata 2 NA NA 1 NA
Chlorophyta Ulvophyceae Ulvales-relatives Ulvales-relatives_X Acrochaete Acrochaete_leptochaete 2 3 6 NA 1
Chlorophyta Ulvophyceae Ulvales-relatives Ulvales-relatives_X Dilabifilum Dilabifilum_sp. 1 1 NA NA NA
Cryptophyta Cryptophyceae Cryptomonadales Cryptomonadales_X Geminigera Geminigera_cryophila 19 18 17 22 8
Cryptophyta Cryptophyceae Cryptomonadales Cryptomonadales_X Hemiselmis Hemiselmis_tepida 2 4 3 NA NA
Haptophyta Prymnesiophyceae Phaeocystales Phaeocystaceae Phaeocystis Phaeocystis_antarctica 19 18 17 22 20
Haptophyta Prymnesiophyceae Phaeocystales Phaeocystaceae Phaeocystis Phaeocystis_sp. 1 NA 1 12 2
Haptophyta Prymnesiophyceae Prymnesiales Chrysochromulinaceae Chrysochromulina Chrysochromulina_sp. 3 9 9 22 5
Ochrophyta Bacillariophyta Bacillariophyta_X Araphid-pennate Asteroplanus Asteroplanus_karianus 19 18 17 20 3
Ochrophyta Bacillariophyta Bacillariophyta_X Araphid-pennate Grammonema Grammonema_striatula 2 NA 3 NA NA
Ochrophyta Bacillariophyta Bacillariophyta_X Araphid-pennate Licmophora Licmophora_grandis 7 1 NA NA NA
Ochrophyta Bacillariophyta Bacillariophyta_X Araphid-pennate Pteroncola Pteroncola_inane 7 1 3 NA NA
Ochrophyta Bacillariophyta Bacillariophyta_X Araphid-pennate Synedra Synedra_hyperborea 2 NA NA NA NA
Ochrophyta Bacillariophyta Bacillariophyta_X Araphid-pennate Synedropsis Synedropsis_recta 1 NA NA NA NA
Ochrophyta Bacillariophyta Bacillariophyta_X Araphid-pennate Tabularia Tabularia_tabulata 1 NA NA NA NA
Ochrophyta Bacillariophyta Bacillariophyta_X Araphid-pennate Thalassiothrix Thalassiothrix_longissima 1 NA NA NA NA
Ochrophyta Bacillariophyta Bacillariophyta_X Polar-centric-Mediophyceae Chaetoceros Chaetoceros_debilis_2 1 NA NA NA NA
Ochrophyta Bacillariophyta Bacillariophyta_X Polar-centric-Mediophyceae Chaetoceros Chaetoceros_neogracilis 19 18 17 16 19
Ochrophyta Bacillariophyta Bacillariophyta_X Polar-centric-Mediophyceae Chaetoceros Chaetoceros_peruvianus 1 2 1 NA NA
Ochrophyta Bacillariophyta Bacillariophyta_X Polar-centric-Mediophyceae Chaetoceros Chaetoceros_rostratus 2 NA NA NA NA
Ochrophyta Bacillariophyta Bacillariophyta_X Polar-centric-Mediophyceae Chaetoceros Chaetoceros_socialis 18 14 7 3 3
Ochrophyta Bacillariophyta Bacillariophyta_X Polar-centric-Mediophyceae Eucampia Eucampia_antarctica 2 2 1 NA NA
Ochrophyta Bacillariophyta Bacillariophyta_X Polar-centric-Mediophyceae Minidiscus Minidiscus_sp. 19 18 17 22 10
Ochrophyta Bacillariophyta Bacillariophyta_X Polar-centric-Mediophyceae Odontella Odontella_aurita 2 NA 1 NA NA
Ochrophyta Bacillariophyta Bacillariophyta_X Polar-centric-Mediophyceae Odontella Odontella_mobiliensis 1 NA NA NA NA
Ochrophyta Bacillariophyta Bacillariophyta_X Polar-centric-Mediophyceae Porosira Porosira_glacialis 19 18 17 2 1
Ochrophyta Bacillariophyta Bacillariophyta_X Polar-centric-Mediophyceae Porosira Porosira_pseudodelicatula 4 1 NA NA NA
Ochrophyta Bacillariophyta Bacillariophyta_X Polar-centric-Mediophyceae Porosira Porosira_pseudodenticulata 1 NA NA NA NA
Ochrophyta Bacillariophyta Bacillariophyta_X Polar-centric-Mediophyceae Shionodiscus Shionodiscus_ritscheri 12 2 NA NA NA
Ochrophyta Bacillariophyta Bacillariophyta_X Polar-centric-Mediophyceae Thalassiosira Thalassiosira_antarctica 1 NA 1 NA NA
Ochrophyta Bacillariophyta Bacillariophyta_X Polar-centric-Mediophyceae Thalassiosira Thalassiosira_minima 19 18 17 21 11
Ochrophyta Bacillariophyta Bacillariophyta_X Polar-centric-Mediophyceae Thalassiosira Thalassiosira_oceanica 1 NA NA NA NA
Ochrophyta Bacillariophyta Bacillariophyta_X Polar-centric-Mediophyceae Thalassiosira Thalassiosira_sp. 19 17 17 14 2
Ochrophyta Bacillariophyta Bacillariophyta_X Polar-centric-Mediophyceae Thalassiosira Thalassiosira_tumida 1 1 NA NA NA
Ochrophyta Bacillariophyta Bacillariophyta_X Radial-centric-basal-Coscinodiscophyceae Actinocyclus Actinocyclus_actinochilus 11 2 2 NA NA
Ochrophyta Bacillariophyta Bacillariophyta_X Radial-centric-basal-Coscinodiscophyceae Corethron Corethron_inerme 19 18 17 NA 1
Ochrophyta Bacillariophyta Bacillariophyta_X Radial-centric-basal-Coscinodiscophyceae Proboscia Proboscia_alata 7 5 8 NA NA
Ochrophyta Bacillariophyta Bacillariophyta_X Radial-centric-basal-Coscinodiscophyceae Proboscia Proboscia_inermis 1 NA NA NA NA
Ochrophyta Bacillariophyta Bacillariophyta_X Radial-centric-basal-Coscinodiscophyceae Rhizosolenia Rhizosolenia_fallax 1 1 NA NA NA
Ochrophyta Bacillariophyta Bacillariophyta_X Radial-centric-basal-Coscinodiscophyceae Rhizosolenia Rhizosolenia_imbricata_var_shrubsolei 1 NA NA NA NA
Ochrophyta Bacillariophyta Bacillariophyta_X Radial-centric-basal-Coscinodiscophyceae Stellarima Stellarima_microtrias 3 1 NA NA NA
Ochrophyta Bacillariophyta Bacillariophyta_X Raphid-pennate Achnanthes Achnanthes_bongranii 1 NA NA NA NA
Ochrophyta Bacillariophyta Bacillariophyta_X Raphid-pennate Amphora Amphora_proteus 12 2 NA NA NA
Ochrophyta Bacillariophyta Bacillariophyta_X Raphid-pennate Cocconeis Cocconeis_stauroneiformis 1 NA NA NA NA
Ochrophyta Bacillariophyta Bacillariophyta_X Raphid-pennate Cymbella Cymbella_gastroides 7 3 9 NA NA
Ochrophyta Bacillariophyta Bacillariophyta_X Raphid-pennate Cymbella Cymbella_laevis 2 NA NA NA NA
Ochrophyta Bacillariophyta Bacillariophyta_X Raphid-pennate Cymbella Cymbella_salina 1 NA NA NA NA
Ochrophyta Bacillariophyta Bacillariophyta_X Raphid-pennate Dickieia Dickieia_ulvacea 4 NA NA NA NA
Ochrophyta Bacillariophyta Bacillariophyta_X Raphid-pennate Encyonema Encyonema_sp. 6 1 6 NA NA
Ochrophyta Bacillariophyta Bacillariophyta_X Raphid-pennate Fragilariopsis Fragilariopsis_cylindrus 19 18 17 22 20
Ochrophyta Bacillariophyta Bacillariophyta_X Raphid-pennate Fragilariopsis Fragilariopsis_sublineata 11 4 17 6 1
Ochrophyta Bacillariophyta Bacillariophyta_X Raphid-pennate Gyrosigma Gyrosigma_limosum 1 NA NA NA NA
Ochrophyta Bacillariophyta Bacillariophyta_X Raphid-pennate Haslea Haslea_spicula 3 2 2 NA NA
Ochrophyta Bacillariophyta Bacillariophyta_X Raphid-pennate Navicula Navicula_phyllepta 1 NA NA NA NA
Ochrophyta Bacillariophyta Bacillariophyta_X Raphid-pennate Navicula Navicula_sp. 4 2 1 NA NA
Ochrophyta Bacillariophyta Bacillariophyta_X Raphid-pennate Naviculales Naviculales_sp. 4 8 11 4 2
Ochrophyta Bacillariophyta Bacillariophyta_X Raphid-pennate Pinnularia Pinnularia_microstauron 1 NA NA NA NA
Ochrophyta Bacillariophyta Bacillariophyta_X Raphid-pennate Pleurosigma Pleurosigma_intermedium 3 1 2 NA NA
Ochrophyta Bacillariophyta Bacillariophyta_X Raphid-pennate Pseudo-nitzschia Pseudo-nitzschia_seriata 15 10 16 6 1
Ochrophyta Bacillariophyta Bacillariophyta_X Raphid-pennate Pseudogomphonema Pseudogomphonema_sp. 10 5 6 NA NA
Ochrophyta Bolidophyceae Parmales Parmales_env_3 Parmales_env_3A Parmales_env_3A_sp. 2 10 NA NA NA
Ochrophyta Bolidophyceae Parmales Parmales_env_3 Parmales_env_3B Parmales_env_3B_sp. 17 18 17 21 15
Ochrophyta Bolidophyceae Parmales Triparmaceae Triparma Triparma_laevis_clade 19 18 17 11 17
Ochrophyta Chrysophyceae Chrysophyceae_X Chrysophyceae_Clade-F Paraphysomonas Paraphysomonas_imperforata 1 3 2 NA NA
Ochrophyta Dictyochophyceae Dictyochophyceae_X Dictyochales Dictyocha Dictyocha_speculum 1 NA NA NA NA
Ochrophyta Dictyochophyceae Dictyochophyceae_X Florenciellales Florenciella Florenciella_parvula 7 15 15 9 NA
Ochrophyta Dictyochophyceae Dictyochophyceae_X Florenciellales Pseudochattonella Pseudochattonella_farcimen 6 13 16 9 NA
Ochrophyta Dictyochophyceae Dictyochophyceae_X Florenciellales Pseudochattonella Pseudochattonella_sp. 1 1 5 2 NA
Ochrophyta Pelagophyceae Pelagomonadales Pelagomonadaceae Pelagomonas Pelagomonas_calceolata 3 11 4 3 18
Ochrophyta Phaeophyceae Phaeophyceae_X Phaeophyceae_XX Desmarestia Desmarestia_menziesii 14 4 11 3 NA
Ochrophyta Phaeophyceae Phaeophyceae_X Phaeophyceae_XX Desmarestia Desmarestia_sp. 13 4 9 3 NA
Ochrophyta Phaeophyceae Phaeophyceae_X Phaeophyceae_XX Ectocarpus Ectocarpus_siliculosus 4 NA 1 2 NA
Ochrophyta Phaeophyceae Phaeophyceae_X Phaeophyceae_XX Phaeurus Phaeurus_antarcticus 16 9 15 7 NA
Ochrophyta Phaeophyceae Phaeophyceae_X Phaeophyceae_XX Pylaiella Pylaiella_littoralis 1 NA 1 NA NA
Rhodophyta Florideophyceae Ceramiales Callithamniaceae Diapse Diapse_ptilota 1 NA NA NA NA
Rhodophyta Florideophyceae Ceramiales Delesseriaceae Phycodrys Phycodrys_rubens 4 NA 1 NA NA
Rhodophyta Florideophyceae Ceramiales Sarcomeniaceae Platysiphonia Platysiphonia_victoriae 1 NA NA NA NA
Rhodophyta Florideophyceae Colaconematales Colaconematales_X Palmaria Palmaria_palmata 1 3 3 NA NA
Rhodophyta Florideophyceae Corallinales Corallinales_X Hapalidiaceae Hapalidiaceae_sp. 6 1 NA NA NA
Rhodophyta Florideophyceae Corallinales Corallinales_X Mesophyllum Mesophyllum_sp. 17 10 14 NA NA
Rhodophyta Florideophyceae Corallinales Corallinales_X Synarthrophyton Synarthrophyton_patena 8 1 1 NA NA
Rhodophyta Florideophyceae Gigartinales Gigartinales_X Chondrus Chondrus_nipponicus 18 7 16 NA NA
Rhodophyta Florideophyceae Gigartinales Gigartinales_X Schottera Schottera_nicaeensis 1 NA NA NA NA
Rhodophyta Florideophyceae Gigartinales Gigartinales_X Stenogramme Stenogramme_interrupta 3 NA 2 NA NA
Rhodophyta Florideophyceae Gracilariales Gracilariales_X Curdiea Curdiea_codiodes 7 1 3 NA NA
Rhodophyta Florideophyceae Plocamiales Plocamiales_X Trematocarpus Trematocarpus_fragilis 7 1 1 NA NA
Chlorophyta Chlorophyceae Chaetopeltidales Chaetopeltidaceae Planophila Planophila_sp. NA 1 NA NA NA
Chlorophyta Chlorophyceae Chlamydomonadales Chlamydomonadales_X Chlamydomonas Chlamydomonas_acidophila NA 1 NA NA NA
Chlorophyta Chlorophyceae Chlamydomonadales Chlamydomonadales_X Chlamydomonas Chlamydomonas_hedleyi NA 1 1 NA NA
Chlorophyta Chlorophyceae Chlamydomonadales Chlamydomonadales_X Haematococcus Haematococcus_zimbabwiensis NA 1 NA NA NA
Chlorophyta Mamiellophyceae Mamiellales Mamiellaceae Mantoniella Mantoniella_squamata NA 1 NA 1 NA
Chlorophyta Mamiellophyceae Mamiellales Mamiellaceae Micromonas Micromonas_clade_B3 NA 8 NA NA 21
Cryptophyta Cryptophyceae Cryptomonadales Cryptomonadales_X Teleaulax Teleaulax_sp. NA 1 NA NA NA
Ochrophyta Bacillariophyta Bacillariophyta_X Araphid-pennate Thalassionema Thalassionema_frauenfeldii NA 1 1 NA NA
Ochrophyta Bacillariophyta Bacillariophyta_X Polar-centric-Mediophyceae Minidiscus Minidiscus_trioculatus NA 2 5 NA NA
Ochrophyta Bacillariophyta Bacillariophyta_X Raphid-pennate Nitzschia Nitzschia_dissipata NA 1 NA NA NA
Ochrophyta Bacillariophyta Bacillariophyta_X Raphid-pennate Pauliella Pauliella_toeniata NA 1 NA NA NA
Ochrophyta Chrysophyceae Chrysophyceae_X Chrysophyceae_Clade-C Spumella Spumella_elongata NA 5 NA NA NA
Ochrophyta Dictyochophyceae Dictyochophyceae_X Pedinellales Pseudopedinella Pseudopedinella_sp. NA 1 NA NA NA
Rhodophyta Florideophyceae Ceramiales Delesseriaceae Hemineura Hemineura_frondosa NA 1 NA NA NA
Rhodophyta Florideophyceae Halymeniales Halymeniales_X Pachymenia Pachymenia_orbicularis NA 1 NA NA NA
Chlorophyta Trebouxiophyceae Prasiolales Prasiolales_X Desmococcus Desmococcus_endolithicus NA NA 1 NA NA
Chlorophyta Trebouxiophyceae Watanabea-Clade Watanabea-Clade_X Chloroidium Chloroidium_ellipsoideum NA NA 1 NA NA
Cryptophyta Cryptophyceae Cryptomonadales Cryptomonadales_X Falcomonas Falcomonas_sp. NA NA 2 NA NA
Haptophyta Prymnesiophyceae Phaeocystales Phaeocystaceae Phaeocystis Phaeocystis_rex NA NA 1 1 1
Ochrophyta Bacillariophyta Bacillariophyta_X Polar-centric-Mediophyceae Hemiaulus Hemiaulus_sinensis NA NA 1 NA NA
Ochrophyta Bacillariophyta Bacillariophyta_X Polar-centric-Mediophyceae Thalassiosira Thalassiosira_minuscula NA NA 1 NA NA
Ochrophyta Bacillariophyta Bacillariophyta_X Polar-centric-Mediophyceae Thalassiosira Thalassiosira_oestrupii NA NA 1 1 NA
Ochrophyta Bacillariophyta Bacillariophyta_X Raphid-pennate Cylindrotheca Cylindrotheca_closterium NA NA 1 NA NA
Ochrophyta Bacillariophyta Bacillariophyta_X Raphid-pennate Navicula Navicula_perminuta NA NA 1 NA NA
Ochrophyta Bacillariophyta Bacillariophyta_X Raphid-pennate Nitzschia Nitzschia_sp. NA NA 1 NA NA
Ochrophyta Bacillariophyta Bacillariophyta_X Raphid-pennate Pseudo-nitzschia Pseudo-nitzschia_turgidula NA NA 1 NA NA
Ochrophyta Bolidophyceae Parmales Triparmaceae Triparma Triparma_laevis_f._inornata NA NA 1 NA NA
Ochrophyta Phaeophyceae Phaeophyceae_X Phaeophyceae_XX Saccharina Saccharina_japonica NA NA 1 NA NA
Cryptophyta Cryptophyceae Cryptomonadales Cryptomonadales_X Falcomonas Falcomonas_daucoides NA NA NA 3 1
Cryptophyta Cryptophyceae Cryptomonadales Cryptomonadales_X Hemiselmis Hemiselmis_sp. NA NA NA 1 NA
Haptophyta Prymnesiophyceae Phaeocystales Phaeocystaceae Phaeocystis Phaeocystis_pouchetii NA NA NA 2 1
Ochrophyta Bacillariophyta Bacillariophyta_X Polar-centric-Mediophyceae Bacterosira Bacterosira_sp. NA NA NA 1 NA
Ochrophyta Bacillariophyta Bacillariophyta_X Raphid-pennate Bacillaria Bacillaria_paxillifer NA NA NA 1 NA
Ochrophyta Bacillariophyta Bacillariophyta_X Raphid-pennate Luka_AeN707 Luka_AeN707-96_sp. NA NA NA 2 1
Ochrophyta Bacillariophyta Bacillariophyta_X Raphid-pennate Pseudo-nitzschia Pseudo-nitzschia_sp. NA NA NA 2 1
Ochrophyta Dictyochophyceae Dictyochophyceae_X Florenciellales Pseudochattonella Pseudochattonella_verruculosa NA NA NA 1 NA
Ochrophyta Bacillariophyta Bacillariophyta_X Polar-centric-Mediophyceae Skeletonema Skeletonema_sp. NA NA NA NA 1
Ochrophyta Pelagophyceae Pelagomonadales Pelagomonadaceae Pelagomonadaceae_clade_A Pelagomonadaceae_clade_A_sp. NA NA NA NA 2
Ochrophyta Pelagophyceae Sarcinochrysidales Sarcinochrysidaceae Ankylochrysis Ankylochrysis_sp. NA NA NA NA 1
Ochrophyta Pelagophyceae Sarcinochrysidales Sarcinochrysidaceae Sarcinochrysis Sarcinochrysis_marina NA NA NA NA 1

png 
  2 

Comparison of species found in the different fractions for 18S filter

  • Compute table of number of samples for each species (rows) vs the three fractions (columns)

  • Only keep

    • Genera that do not contain _X
  • We consider now ALL samples (will need to remove samples for which the > 20 um is missing)

division class > 20 um 0.2-3 um 3-20 um
Chlorophyta Chlorophyceae 8 6 6
Chlorophyta Mamiellophyceae 31 43 44
Chlorophyta Palmophyllophyceae 5 26 25
Chlorophyta Pyramimonadophyceae 29 39 44
Chlorophyta Trebouxiophyceae 9 1 7
Chlorophyta Ulvophyceae 29 27 29
Cryptophyta Cryptophyceae 36 43 44
Haptophyta Prymnesiophyceae 33 43 43
Ochrophyta Bacillariophyta 36 43 44
Ochrophyta Bolidophyceae 35 43 44
Ochrophyta Chrysophyceae 29 42 42
Ochrophyta Dictyochophyceae 28 43 44
Ochrophyta MOCH-1 1 3 4
Ochrophyta MOCH-2 15 24 36
Ochrophyta Pelagophyceae 35 43 44
Ochrophyta Phaeophyceae 34 34 43
Ochrophyta Xanthophyceae 1 NA NA
Rhodophyta Bangiophyceae 2 1 NA
Rhodophyta Florideophyceae 35 37 43
division class order family genus species > 20 um 0.2-3 um 3-20 um
Chlorophyta Chlorophyceae Chlamydomonadales Chlamydomonadales_X Chlamydomonas Chlamydomonas_hedleyi 1 1 1
Chlorophyta Chlorophyceae Chlamydomonadales Chlamydomonadales_X Chlamydomonas Chlamydomonas_kuwadae 5 3 4
Chlorophyta Chlorophyceae Chlamydomonadales Chlamydomonadales_X Chlamydomonas Chlamydomonas_raudensis 1 NA 1
Chlorophyta Chlorophyceae Chlamydomonadales Chlamydomonadales_X Pleurastrum Pleurastrum_sp. 1 1 2
Chlorophyta Chlorophyceae Sphaeropleales Sphaeropleales_X Radiococcus Radiococcus_polycoccus 1 NA NA
Chlorophyta Mamiellophyceae Dolichomastigales Dolichomastigaceae Dolichomastigaceae-B Dolichomastigaceae-B_sp. 15 26 27
Chlorophyta Mamiellophyceae Mamiellales Bathycoccaceae Bathycoccus Bathycoccus_prasinos 14 41 41
Chlorophyta Mamiellophyceae Mamiellales Mamiellaceae Micromonas Micromonas_clade_B3 2 20 4
Chlorophyta Mamiellophyceae Mamiellales Mamiellaceae Micromonas Micromonas_polaris 26 42 41
Chlorophyta Palmophyllophyceae Prasinococcales Prasinococcales-Clade-B Prasinoderma Prasinoderma_sp. 5 26 25
Chlorophyta Pyramimonadophyceae Pyramimonadales Pyramimonadaceae Pyramimonas Pyramimonas_australis 17 29 35
Chlorophyta Pyramimonadophyceae Pyramimonadales Pyramimonadaceae Pyramimonas Pyramimonas_gelidicola 28 39 44
Chlorophyta Trebouxiophyceae Chlorellales Chlorellales_X Chlorella Chlorella_sorokiniana 1 NA NA
Chlorophyta Trebouxiophyceae Prasiolales Prasiolales_X Koliella Koliella_sempervirens 1 NA NA
Chlorophyta Trebouxiophyceae Watanabea-Clade Watanabea-Clade_X Chloroidium Chloroidium_saccharophila 2 1 1
Chlorophyta Ulvophyceae Ulotrichales Ulotrichales_X Chlorothrix Chlorothrix_sp. 16 5 8
Chlorophyta Ulvophyceae Ulotrichales Ulotrichales_X Monostroma Monostroma_grevillei 12 11 14
Chlorophyta Ulvophyceae Ulotrichales Ulotrichales_X Ulothrix Ulothrix_zonata 2 2 1
Chlorophyta Ulvophyceae Ulvales-relatives Ulvales-relatives_X Acrochaete Acrochaete_leptochaete 5 8 13
Chlorophyta Ulvophyceae Ulvales-relatives Ulvales-relatives_X Dilabifilum Dilabifilum_sp. 3 5 5
Cryptophyta Cryptophyceae Cryptomonadales Cryptomonadales_X Geminigera Geminigera_cryophila 36 43 44
Cryptophyta Cryptophyceae Cryptomonadales Cryptomonadales_X Hemiselmis Hemiselmis_tepida 2 7 7
Haptophyta Prymnesiophyceae Phaeocystales Phaeocystaceae Phaeocystis Phaeocystis_antarctica 33 43 43
Haptophyta Prymnesiophyceae Phaeocystales Phaeocystaceae Phaeocystis Phaeocystis_sp. 1 NA 1
Haptophyta Prymnesiophyceae Prymnesiales Chrysochromulinaceae Chrysochromulina Chrysochromulina_sp. 6 23 31
Ochrophyta Bacillariophyta Bacillariophyta_X Araphid-pennate Asteroplanus Asteroplanus_karianus 35 39 43
Ochrophyta Bacillariophyta Bacillariophyta_X Araphid-pennate Grammonema Grammonema_striatula 9 2 8
Ochrophyta Bacillariophyta Bacillariophyta_X Araphid-pennate Licmophora Licmophora_grandis 17 1 1
Ochrophyta Bacillariophyta Bacillariophyta_X Araphid-pennate Pteroncola Pteroncola_inane 8 1 4
Ochrophyta Bacillariophyta Bacillariophyta_X Araphid-pennate Synedra Synedra_hyperborea 2 1 NA
Ochrophyta Bacillariophyta Bacillariophyta_X Araphid-pennate Synedropsis Synedropsis_recta 1 NA NA
Ochrophyta Bacillariophyta Bacillariophyta_X Araphid-pennate Tabularia Tabularia_tabulata 1 NA NA
Ochrophyta Bacillariophyta Bacillariophyta_X Araphid-pennate Thalassionema Thalassionema_frauenfeldii 2 1 2
Ochrophyta Bacillariophyta Bacillariophyta_X Araphid-pennate Thalassiothrix Thalassiothrix_longissima 4 2 3
Ochrophyta Bacillariophyta Bacillariophyta_X Polar-centric-Mediophyceae Chaetoceros Chaetoceros_danicus 4 1 1
Ochrophyta Bacillariophyta Bacillariophyta_X Polar-centric-Mediophyceae Chaetoceros Chaetoceros_debilis_2 12 9 9
Ochrophyta Bacillariophyta Bacillariophyta_X Polar-centric-Mediophyceae Chaetoceros Chaetoceros_dichaeta 3 3 2
Ochrophyta Bacillariophyta Bacillariophyta_X Polar-centric-Mediophyceae Chaetoceros Chaetoceros_neogracilis 33 38 43
Ochrophyta Bacillariophyta Bacillariophyta_X Polar-centric-Mediophyceae Chaetoceros Chaetoceros_peruvianus 2 3 3
Ochrophyta Bacillariophyta Bacillariophyta_X Polar-centric-Mediophyceae Chaetoceros Chaetoceros_rostratus 10 3 7
Ochrophyta Bacillariophyta Bacillariophyta_X Polar-centric-Mediophyceae Chaetoceros Chaetoceros_socialis 25 22 14
Ochrophyta Bacillariophyta Bacillariophyta_X Polar-centric-Mediophyceae Ditylum Ditylum_sol 2 1 1
Ochrophyta Bacillariophyta Bacillariophyta_X Polar-centric-Mediophyceae Eucampia Eucampia_antarctica 14 14 11
Ochrophyta Bacillariophyta Bacillariophyta_X Polar-centric-Mediophyceae Hemiaulus Hemiaulus_sinensis 3 3 6
Ochrophyta Bacillariophyta Bacillariophyta_X Polar-centric-Mediophyceae Minidiscus Minidiscus_sp. 36 42 44
Ochrophyta Bacillariophyta Bacillariophyta_X Polar-centric-Mediophyceae Minidiscus Minidiscus_trioculatus 1 2 12
Ochrophyta Bacillariophyta Bacillariophyta_X Polar-centric-Mediophyceae Odontella Odontella_aurita 2 NA 1
Ochrophyta Bacillariophyta Bacillariophyta_X Polar-centric-Mediophyceae Odontella Odontella_mobiliensis 4 NA NA
Ochrophyta Bacillariophyta Bacillariophyta_X Polar-centric-Mediophyceae Porosira Porosira_glacialis 36 43 42
Ochrophyta Bacillariophyta Bacillariophyta_X Polar-centric-Mediophyceae Porosira Porosira_pseudodelicatula 4 2 NA
Ochrophyta Bacillariophyta Bacillariophyta_X Polar-centric-Mediophyceae Porosira Porosira_pseudodenticulata 2 NA 1
Ochrophyta Bacillariophyta Bacillariophyta_X Polar-centric-Mediophyceae Shionodiscus Shionodiscus_ritscheri 20 3 4
Ochrophyta Bacillariophyta Bacillariophyta_X Polar-centric-Mediophyceae Thalassiosira Thalassiosira_antarctica 1 NA 1
Ochrophyta Bacillariophyta Bacillariophyta_X Polar-centric-Mediophyceae Thalassiosira Thalassiosira_minima 35 41 44
Ochrophyta Bacillariophyta Bacillariophyta_X Polar-centric-Mediophyceae Thalassiosira Thalassiosira_oceanica 1 1 1
Ochrophyta Bacillariophyta Bacillariophyta_X Polar-centric-Mediophyceae Thalassiosira Thalassiosira_rotula 1 NA 1
Ochrophyta Bacillariophyta Bacillariophyta_X Polar-centric-Mediophyceae Thalassiosira Thalassiosira_sp. 33 37 36
Ochrophyta Bacillariophyta Bacillariophyta_X Polar-centric-Mediophyceae Thalassiosira Thalassiosira_tumida 12 1 2
Ochrophyta Bacillariophyta Bacillariophyta_X Radial-centric-basal-Coscinodiscophyceae Actinocyclus Actinocyclus_actinochilus 23 5 4
Ochrophyta Bacillariophyta Bacillariophyta_X Radial-centric-basal-Coscinodiscophyceae Actinocyclus Actinocyclus_curvatulus 5 2 1
Ochrophyta Bacillariophyta Bacillariophyta_X Radial-centric-basal-Coscinodiscophyceae Asteromphalus Asteromphalus_sp. 2 NA NA
Ochrophyta Bacillariophyta Bacillariophyta_X Radial-centric-basal-Coscinodiscophyceae Corethron Corethron_inerme 36 42 43
Ochrophyta Bacillariophyta Bacillariophyta_X Radial-centric-basal-Coscinodiscophyceae Coscinodiscus Coscinodiscus_concinnus 1 NA NA
Ochrophyta Bacillariophyta Bacillariophyta_X Radial-centric-basal-Coscinodiscophyceae Coscinodiscus Coscinodiscus_jonesianus 1 NA NA
Ochrophyta Bacillariophyta Bacillariophyta_X Radial-centric-basal-Coscinodiscophyceae Guinardia Guinardia_solstherfothii 1 NA 1
Ochrophyta Bacillariophyta Bacillariophyta_X Radial-centric-basal-Coscinodiscophyceae Proboscia Proboscia_alata 19 12 23
Ochrophyta Bacillariophyta Bacillariophyta_X Radial-centric-basal-Coscinodiscophyceae Proboscia Proboscia_inermis 1 NA NA
Ochrophyta Bacillariophyta Bacillariophyta_X Radial-centric-basal-Coscinodiscophyceae Rhizosolenia Rhizosolenia_fallax 1 1 2
Ochrophyta Bacillariophyta Bacillariophyta_X Radial-centric-basal-Coscinodiscophyceae Rhizosolenia Rhizosolenia_imbricata_var_shrubsolei 2 NA NA
Ochrophyta Bacillariophyta Bacillariophyta_X Radial-centric-basal-Coscinodiscophyceae Stellarima Stellarima_microtrias 10 4 2
Ochrophyta Bacillariophyta Bacillariophyta_X Raphid-pennate Achnanthes Achnanthes_bongranii 3 NA 2
Ochrophyta Bacillariophyta Bacillariophyta_X Raphid-pennate Amphora Amphora_proteus 18 3 3
Ochrophyta Bacillariophyta Bacillariophyta_X Raphid-pennate Cocconeis Cocconeis_stauroneiformis 1 1 NA
Ochrophyta Bacillariophyta Bacillariophyta_X Raphid-pennate Cymbella Cymbella_gastroides 10 7 21
Ochrophyta Bacillariophyta Bacillariophyta_X Raphid-pennate Cymbella Cymbella_laevis 3 NA NA
Ochrophyta Bacillariophyta Bacillariophyta_X Raphid-pennate Cymbella Cymbella_salina 1 NA NA
Ochrophyta Bacillariophyta Bacillariophyta_X Raphid-pennate Dickieia Dickieia_ulvacea 4 1 1
Ochrophyta Bacillariophyta Bacillariophyta_X Raphid-pennate Encyonema Encyonema_sp. 12 4 8
Ochrophyta Bacillariophyta Bacillariophyta_X Raphid-pennate Fragilariopsis Fragilariopsis_cylindrus 36 43 44
Ochrophyta Bacillariophyta Bacillariophyta_X Raphid-pennate Fragilariopsis Fragilariopsis_sublineata 14 7 29
Ochrophyta Bacillariophyta Bacillariophyta_X Raphid-pennate Gyrosigma Gyrosigma_limosum 1 NA NA
Ochrophyta Bacillariophyta Bacillariophyta_X Raphid-pennate Haslea Haslea_spicula 11 12 14
Ochrophyta Bacillariophyta Bacillariophyta_X Raphid-pennate Navicula Navicula_lanceolata 1 NA NA
Ochrophyta Bacillariophyta Bacillariophyta_X Raphid-pennate Navicula Navicula_phyllepta 1 NA NA
Ochrophyta Bacillariophyta Bacillariophyta_X Raphid-pennate Navicula Navicula_sp. 10 7 9
Ochrophyta Bacillariophyta Bacillariophyta_X Raphid-pennate Naviculales Naviculales_sp. 4 11 15
Ochrophyta Bacillariophyta Bacillariophyta_X Raphid-pennate Pinnularia Pinnularia_microstauron 1 NA NA
Ochrophyta Bacillariophyta Bacillariophyta_X Raphid-pennate Pleurosigma Pleurosigma_intermedium 3 1 2
Ochrophyta Bacillariophyta Bacillariophyta_X Raphid-pennate Pseudo-nitzschia Pseudo-nitzschia_seriata 30 22 32
Ochrophyta Bacillariophyta Bacillariophyta_X Raphid-pennate Pseudogomphonema Pseudogomphonema_sp. 12 6 7
Ochrophyta Bolidophyceae Parmales Parmales_env_3 Parmales_env_3A Parmales_env_3A_sp. 5 28 12
Ochrophyta Bolidophyceae Parmales Parmales_env_3 Parmales_env_3B Parmales_env_3B_sp. 29 42 42
Ochrophyta Bolidophyceae Parmales Triparmaceae Triparma Triparma_laevis_clade 35 42 44
Ochrophyta Chrysophyceae Chrysophyceae_X Chrysophyceae_Clade-C Pedospumella Pedospumella_encystans 1 1 NA
Ochrophyta Chrysophyceae Chrysophyceae_X Chrysophyceae_Clade-C Spumella Spumella_elongata 2 13 7
Ochrophyta Chrysophyceae Chrysophyceae_X Chrysophyceae_Clade-F Paraphysomonas Paraphysomonas_butcheri 1 4 3
Ochrophyta Chrysophyceae Chrysophyceae_X Chrysophyceae_Clade-F Paraphysomonas Paraphysomonas_imperforata 3 8 4
Ochrophyta Dictyochophyceae Dictyochophyceae_X Dictyochales Dictyocha Dictyocha_speculum 2 5 4
Ochrophyta Dictyochophyceae Dictyochophyceae_X Florenciellales Florenciella Florenciella_parvula 13 38 41
Ochrophyta Dictyochophyceae Dictyochophyceae_X Florenciellales Pseudochattonella Pseudochattonella_farcimen 10 32 43
Ochrophyta Dictyochophyceae Dictyochophyceae_X Florenciellales Pseudochattonella Pseudochattonella_sp. 3 10 13
Ochrophyta Pelagophyceae Pelagomonadales Pelagomonadaceae Pelagomonas Pelagomonas_calceolata 6 28 16
Ochrophyta Phaeophyceae Phaeophyceae_X Phaeophyceae_XX Desmarestia Desmarestia_menziesii 23 9 17
Ochrophyta Phaeophyceae Phaeophyceae_X Phaeophyceae_XX Desmarestia Desmarestia_sp. 20 16 23
Ochrophyta Phaeophyceae Phaeophyceae_X Phaeophyceae_XX Ectocarpus Ectocarpus_siliculosus 8 2 3
Ochrophyta Phaeophyceae Phaeophyceae_X Phaeophyceae_XX Phaeurus Phaeurus_antarcticus 28 10 21
Ochrophyta Phaeophyceae Phaeophyceae_X Phaeophyceae_XX Pylaiella Pylaiella_littoralis 4 NA 2
Ochrophyta Phaeophyceae Phaeophyceae_X Phaeophyceae_XX Saccharina Saccharina_japonica 1 2 6
Ochrophyta Xanthophyceae Xanthophyceae_X Xanthophyceae_XX Botrydiopsis Botrydiopsis_callosa 1 NA NA
Rhodophyta Bangiophyceae Bangiales Bangiaceae Porphyra Porphyra_plocamiestris 1 NA NA
Rhodophyta Bangiophyceae Bangiales Bangiaceae Pyropia Pyropia_sp. 1 NA NA
Rhodophyta Florideophyceae Ceramiales Callithamniaceae Diapse Diapse_ptilota 2 1 NA
Rhodophyta Florideophyceae Ceramiales Delesseriaceae Phycodrys Phycodrys_rubens 7 2 7
Rhodophyta Florideophyceae Ceramiales Sarcomeniaceae Platysiphonia Platysiphonia_victoriae 1 1 NA
Rhodophyta Florideophyceae Colaconematales Colaconematales_X Palmaria Palmaria_palmata 14 18 18
Rhodophyta Florideophyceae Corallinales Corallinales_X Hapalidiaceae Hapalidiaceae_sp. 7 2 1
Rhodophyta Florideophyceae Corallinales Corallinales_X Mesophyllum Mesophyllum_sp. 32 22 36
Rhodophyta Florideophyceae Corallinales Corallinales_X Synarthrophyton Synarthrophyton_patena 11 2 1
Rhodophyta Florideophyceae Gigartinales Gigartinales_X Chondrus Chondrus_nipponicus 34 22 41
Rhodophyta Florideophyceae Gigartinales Gigartinales_X Schottera Schottera_nicaeensis 1 NA NA
Rhodophyta Florideophyceae Gigartinales Gigartinales_X Stenogramme Stenogramme_interrupta 4 NA 2
Rhodophyta Florideophyceae Gracilariales Gracilariales_X Curdiea Curdiea_codiodes 14 4 9
Rhodophyta Florideophyceae Plocamiales Plocamiales_X Trematocarpus Trematocarpus_fragilis 10 1 1
Chlorophyta Chlorophyceae Chaetopeltidales Chaetopeltidaceae Planophila Planophila_sp. NA 1 NA
Chlorophyta Chlorophyceae Chlamydomonadales Chlamydomonadales_X Chlamydomonas Chlamydomonas_acidophila NA 1 NA
Chlorophyta Chlorophyceae Chlamydomonadales Chlamydomonadales_X Haematococcus Haematococcus_zimbabwiensis NA 1 NA
Chlorophyta Mamiellophyceae Mamiellales Mamiellaceae Mantoniella Mantoniella_squamata NA 4 1
Cryptophyta Cryptophyceae Cryptomonadales Cryptomonadales_X Plagioselmis Plagioselmis_nannoplanctica NA 1 1
Cryptophyta Cryptophyceae Cryptomonadales Cryptomonadales_X Teleaulax Teleaulax_sp. NA 1 NA
Ochrophyta Bacillariophyta Bacillariophyta_X Polar-centric-Mediophyceae Chaetoceros Chaetoceros_gelidus NA 3 1
Ochrophyta Bacillariophyta Bacillariophyta_X Radial-centric-basal-Coscinodiscophyceae Guinardia Guinardia_delicatula NA 1 2
Ochrophyta Bacillariophyta Bacillariophyta_X Raphid-pennate Nitzschia Nitzschia_dissipata NA 1 NA
Ochrophyta Bacillariophyta Bacillariophyta_X Raphid-pennate Pauliella Pauliella_toeniata NA 1 1
Ochrophyta Bolidophyceae Parmales Triparmaceae Triparma Triparma_sp. NA 6 5
Ochrophyta Dictyochophyceae Dictyochophyceae_X Pedinellales Pseudopedinella Pseudopedinella_sp. NA 1 2
Ochrophyta Dictyochophyceae Dictyochophyceae_X Pedinellales Pteridomonas Pteridomonas_danica NA 1 NA
Ochrophyta Phaeophyceae Phaeophyceae_X Phaeophyceae_XX Desmarestia Desmarestia_anceps NA 1 NA
Rhodophyta Bangiophyceae Bangiales Bangiaceae Pyropia Pyropia_dentata NA 1 NA
Rhodophyta Florideophyceae Ceramiales Dasyaceae Dasya Dasya_collabens NA 1 NA
Rhodophyta Florideophyceae Ceramiales Delesseriaceae Hemineura Hemineura_frondosa NA 1 NA
Rhodophyta Florideophyceae Ceramiales Rhodomelaceae Rhodomela Rhodomela_confervoides NA 1 1
Rhodophyta Florideophyceae Gigartinales Gigartinales_X Kallymenia Kallymenia_tasmanica NA 1 2
Rhodophyta Florideophyceae Halymeniales Halymeniales_X Pachymenia Pachymenia_orbicularis NA 1 NA
Chlorophyta Trebouxiophyceae Prasiolales Prasiolales_X Desmococcus Desmococcus_endolithicus NA NA 1
Chlorophyta Trebouxiophyceae Prasiolales Prasiolales_X Prasiola Prasiola_crispa NA NA 3
Chlorophyta Trebouxiophyceae Watanabea-Clade Watanabea-Clade_X Chloroidium Chloroidium_ellipsoideum NA NA 1
Cryptophyta Cryptophyceae Cryptomonadales Cryptomonadales_X Falcomonas Falcomonas_sp. NA NA 2
Haptophyta Prymnesiophyceae Phaeocystales Phaeocystaceae Phaeocystis Phaeocystis_rex NA NA 1
Ochrophyta Bacillariophyta Bacillariophyta_X Polar-centric-Mediophyceae Porosira Porosira_sp. NA NA 1
Ochrophyta Bacillariophyta Bacillariophyta_X Polar-centric-Mediophyceae Thalassiosira Thalassiosira_minuscula NA NA 1
Ochrophyta Bacillariophyta Bacillariophyta_X Polar-centric-Mediophyceae Thalassiosira Thalassiosira_oestrupii NA NA 2
Ochrophyta Bacillariophyta Bacillariophyta_X Raphid-pennate Cylindrotheca Cylindrotheca_closterium NA NA 1
Ochrophyta Bacillariophyta Bacillariophyta_X Raphid-pennate Navicula Navicula_perminuta NA NA 1
Ochrophyta Bacillariophyta Bacillariophyta_X Raphid-pennate Nitzschia Nitzschia_sp. NA NA 1
Ochrophyta Bacillariophyta Bacillariophyta_X Raphid-pennate Pseudo-nitzschia Pseudo-nitzschia_turgidula NA NA 1
Ochrophyta Bolidophyceae Parmales Triparmaceae Triparma Triparma_laevis_f._inornata NA NA 1
Rhodophyta Florideophyceae Gigartinales Gigartinales_X Delisea Delisea_pulchra NA NA 1

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  2 

Comparison of species found in the different fractions for 18S sort

  • Compute table of number of samples for each species (rows) vs the three fractions (columns)

  • Only keep

    • Genera that do not contain _X
  • We consider now ALL samples (will need to remove samples for which the > 20 um is missing)

division class nano pico
Chlorophyta Chlorophyceae 1 NA
Chlorophyta Mamiellophyceae 18 22
Chlorophyta Palmophyllophyceae 1 1
Chlorophyta Pyramimonadophyceae 19 4
Chlorophyta Ulvophyceae 2 2
Cryptophyta Cryptophyceae 22 9
Haptophyta Prymnesiophyceae 22 22
Ochrophyta Bacillariophyta 22 22
Ochrophyta Bolidophyceae 21 20
Ochrophyta Chrysophyceae 2 2
Ochrophyta Dictyochophyceae 15 1
Ochrophyta MOCH-2 11 NA
Ochrophyta Pelagophyceae 22 22
Ochrophyta Phaeophyceae 10 NA
division class order family genus species nano pico
Chlorophyta Chlorophyceae Chlamydomonadales Chlamydomonadales_X Chlamydomonas Chlamydomonas_raudensis 1 NA
Chlorophyta Mamiellophyceae Dolichomastigales Dolichomastigaceae Dolichomastigaceae-B Dolichomastigaceae-B_sp. 1 5
Chlorophyta Mamiellophyceae Mamiellales Bathycoccaceae Bathycoccus Bathycoccus_prasinos 1 22
Chlorophyta Mamiellophyceae Mamiellales Mamiellaceae Mantoniella Mantoniella_squamata 1 NA
Chlorophyta Mamiellophyceae Mamiellales Mamiellaceae Micromonas Micromonas_polaris 17 22
Chlorophyta Palmophyllophyceae Prasinococcales Prasinococcales-Clade-B Prasinoderma Prasinoderma_sp. 1 1
Chlorophyta Pyramimonadophyceae Pyramimonadales Pyramimonadaceae Pyramimonas Pyramimonas_australis 10 2
Chlorophyta Pyramimonadophyceae Pyramimonadales Pyramimonadaceae Pyramimonas Pyramimonas_gelidicola 19 4
Chlorophyta Ulvophyceae Ulotrichales Ulotrichales_X Monostroma Monostroma_grevillei 2 1
Chlorophyta Ulvophyceae Ulotrichales Ulotrichales_X Ulothrix Ulothrix_zonata 1 NA
Cryptophyta Cryptophyceae Cryptomonadales Cryptomonadales_X Falcomonas Falcomonas_daucoides 3 1
Cryptophyta Cryptophyceae Cryptomonadales Cryptomonadales_X Geminigera Geminigera_cryophila 22 8
Cryptophyta Cryptophyceae Cryptomonadales Cryptomonadales_X Hemiselmis Hemiselmis_sp. 1 NA
Haptophyta Prymnesiophyceae Phaeocystales Phaeocystaceae Phaeocystis Phaeocystis_antarctica 22 20
Haptophyta Prymnesiophyceae Phaeocystales Phaeocystaceae Phaeocystis Phaeocystis_pouchetii 2 1
Haptophyta Prymnesiophyceae Phaeocystales Phaeocystaceae Phaeocystis Phaeocystis_rex 1 1
Haptophyta Prymnesiophyceae Phaeocystales Phaeocystaceae Phaeocystis Phaeocystis_sp. 12 2
Haptophyta Prymnesiophyceae Prymnesiales Chrysochromulinaceae Chrysochromulina Chrysochromulina_sp. 22 5
Ochrophyta Bacillariophyta Bacillariophyta_X Araphid-pennate Asteroplanus Asteroplanus_karianus 20 3
Ochrophyta Bacillariophyta Bacillariophyta_X Polar-centric-Mediophyceae Bacterosira Bacterosira_sp. 1 NA
Ochrophyta Bacillariophyta Bacillariophyta_X Polar-centric-Mediophyceae Chaetoceros Chaetoceros_neogracilis 16 19
Ochrophyta Bacillariophyta Bacillariophyta_X Polar-centric-Mediophyceae Chaetoceros Chaetoceros_socialis 3 3
Ochrophyta Bacillariophyta Bacillariophyta_X Polar-centric-Mediophyceae Minidiscus Minidiscus_sp. 22 10
Ochrophyta Bacillariophyta Bacillariophyta_X Polar-centric-Mediophyceae Porosira Porosira_glacialis 2 1
Ochrophyta Bacillariophyta Bacillariophyta_X Polar-centric-Mediophyceae Thalassiosira Thalassiosira_minima 21 11
Ochrophyta Bacillariophyta Bacillariophyta_X Polar-centric-Mediophyceae Thalassiosira Thalassiosira_oestrupii 1 NA
Ochrophyta Bacillariophyta Bacillariophyta_X Polar-centric-Mediophyceae Thalassiosira Thalassiosira_sp. 14 2
Ochrophyta Bacillariophyta Bacillariophyta_X Raphid-pennate Bacillaria Bacillaria_paxillifer 1 NA
Ochrophyta Bacillariophyta Bacillariophyta_X Raphid-pennate Fragilariopsis Fragilariopsis_cylindrus 22 20
Ochrophyta Bacillariophyta Bacillariophyta_X Raphid-pennate Fragilariopsis Fragilariopsis_sublineata 6 1
Ochrophyta Bacillariophyta Bacillariophyta_X Raphid-pennate Luka_AeN707 Luka_AeN707-96_sp. 2 1
Ochrophyta Bacillariophyta Bacillariophyta_X Raphid-pennate Naviculales Naviculales_sp. 4 2
Ochrophyta Bacillariophyta Bacillariophyta_X Raphid-pennate Pseudo-nitzschia Pseudo-nitzschia_seriata 6 1
Ochrophyta Bacillariophyta Bacillariophyta_X Raphid-pennate Pseudo-nitzschia Pseudo-nitzschia_sp. 2 1
Ochrophyta Bolidophyceae Parmales Parmales_env_3 Parmales_env_3B Parmales_env_3B_sp. 21 15
Ochrophyta Bolidophyceae Parmales Triparmaceae Triparma Triparma_laevis_clade 11 17
Ochrophyta Dictyochophyceae Dictyochophyceae_X Florenciellales Florenciella Florenciella_parvula 9 NA
Ochrophyta Dictyochophyceae Dictyochophyceae_X Florenciellales Pseudochattonella Pseudochattonella_farcimen 9 NA
Ochrophyta Dictyochophyceae Dictyochophyceae_X Florenciellales Pseudochattonella Pseudochattonella_sp. 2 NA
Ochrophyta Dictyochophyceae Dictyochophyceae_X Florenciellales Pseudochattonella Pseudochattonella_verruculosa 1 NA
Ochrophyta Pelagophyceae Pelagomonadales Pelagomonadaceae Pelagomonas Pelagomonas_calceolata 3 18
Ochrophyta Phaeophyceae Phaeophyceae_X Phaeophyceae_XX Desmarestia Desmarestia_menziesii 3 NA
Ochrophyta Phaeophyceae Phaeophyceae_X Phaeophyceae_XX Desmarestia Desmarestia_sp. 3 NA
Ochrophyta Phaeophyceae Phaeophyceae_X Phaeophyceae_XX Ectocarpus Ectocarpus_siliculosus 2 NA
Ochrophyta Phaeophyceae Phaeophyceae_X Phaeophyceae_XX Phaeurus Phaeurus_antarcticus 7 NA
Chlorophyta Mamiellophyceae Mamiellales Mamiellaceae Micromonas Micromonas_clade_B3 NA 21
Chlorophyta Ulvophyceae Ulvales-relatives Ulvales-relatives_X Acrochaete Acrochaete_leptochaete NA 1
Ochrophyta Bacillariophyta Bacillariophyta_X Polar-centric-Mediophyceae Skeletonema Skeletonema_sp. NA 1
Ochrophyta Bacillariophyta Bacillariophyta_X Radial-centric-basal-Coscinodiscophyceae Corethron Corethron_inerme NA 1
Ochrophyta Pelagophyceae Pelagomonadales Pelagomonadaceae Pelagomonadaceae_clade_A Pelagomonadaceae_clade_A_sp. NA 2
Ochrophyta Pelagophyceae Sarcinochrysidales Sarcinochrysidaceae Ankylochrysis Ankylochrysis_sp. NA 1
Ochrophyta Pelagophyceae Sarcinochrysidales Sarcinochrysidaceae Sarcinochrysis Sarcinochrysis_marina NA 1

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Figures

CARBOM code

2019-10-21